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0
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1 ##fileformat=VCFv4.1
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2 ##FILTER=<ID=LowQual,Description="Low quality">
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3 ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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4 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
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5 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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7 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
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8 ##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.7-4-g6f46d11,Date="Fri Nov 01 16:17:42 CET 2013",Epoch=1383319062999,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/scratch/hueber-35211/CATB1.RG.sorted.indelrealigned.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/projects/coffee_snp/donnees_genomiques/pseudomolecules.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=4 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
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9 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
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10 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
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11 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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12 ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
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13 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
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14 ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
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15 ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
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16 ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
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17 ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
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18 ##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
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19 ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
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20 ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
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21 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
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22 ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
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23 ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
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24 ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
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25 ##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
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26 ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
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27 ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
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28 ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
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29 ##contig=<ID=chr1,length=38193400>
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30 ##contig=<ID=chr10,length=27624748>
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31 ##contig=<ID=chr11,length=33540656>
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32 ##contig=<ID=chr2,length=54522928>
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33 ##contig=<ID=chr3,length=32030951>
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34 ##contig=<ID=chr4,length=28191985>
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35 ##contig=<ID=chr5,length=29137935>
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36 ##contig=<ID=chr6,length=37293965>
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37 ##contig=<ID=chr7,length=29833120>
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38 ##contig=<ID=chr8,length=31585744>
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39 ##contig=<ID=chr9,length=22352177>
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40 ##contig=<ID=chr0,length=205603396>
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41 ##reference=file:///data/projects/coffee_snp/donnees_genomiques/pseudomolecules.fasta
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42 ##SnpEffVersion="2.0.5d (build 2012-01-19), by Pablo Cingolani"
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43 ##SnpEffCmd="SnpEff eff coffea /apps/www/sniplay.cirad.fr/data/Coffee/Argemo_genomic.nonannotated.vcf.2 -i VCF -o VCF -c snpEff.config "
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44 ##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effefct_Impact | Functional_Class | Codon_Change | Amino_Acid_change | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' ">
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45 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1
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46 chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0
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47 chr1 2232 . A C 11.83 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.00;MQ0=0;QD=11.83;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0
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48 chr1 2264 . C T 68.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;DP=5;Dels=0.00;FS=10.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.41;MQ0=0;MQRankSum=0.358;QD=13.75;ReadPosRankSum=-1.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:2,3:5:53:97,0,53
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49 chr1 2353 . T A 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.050;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=2.5027;MLEAC=1;MLEAF=0.500;MQ=31.07;MQ0=3;MQRankSum=0.261;QD=1.18;ReadPosRankSum=-1.081;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:19,7:26:59:59,0,409
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50 chr1 2482 . C T 207.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.294;DP=19;Dels=0.00;FS=5.229;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=26.95;MQ0=7;MQRankSum=0.370;QD=10.94;ReadPosRankSum=-1.109;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:5,14:19:83:236,0,83
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51 chr1 2558 . A T 789.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.038;DP=45;Dels=0.00;FS=4.170;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=28.40;MQ0=13;MQRankSum=0.121;QD=17.55;ReadPosRankSum=-0.072;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:13,32:45:99:818,0,101
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52 chr1 2925 . A T 351.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.619;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=5.7776;MLEAC=1;MLEAF=0.500;MQ=38.24;MQ0=1;MQRankSum=0.372;QD=17.59;ReadPosRankSum=-1.362;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:9,11:20:99:380,0,275
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53 chr1 2941 . A G 221.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.936;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.63;MQ0=1;MQRankSum=1.524;QD=14.78;ReadPosRankSum=0.663;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:7,8:15:99:250,0,227
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54 chr1 2985 . T C 73.28 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=18.19;MQ0=8;QD=6.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:7,4:11:9:101,9,0
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55 chr1 3705 . G T 103.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.32;MQ0=0;QD=14.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:12:131,12,0
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56 chr1 3745 . A T 180.84 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.44;MQ0=0;QD=22.60;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,8:8:18:209,18,0
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57 chr1 3864 . C T 33.74 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=12.81;MQ0=4;QD=3.75;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,9:9:6:61,6,0
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58 chr1 3887 . G C 131.9 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.03;MQ0=5;QD=6.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,22:22:15:160,15,0
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59 chr1 3944 . G T 182.84 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.63;MQ0=5;QD=7.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,25:25:18:211,18,0
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60 chr1 4109 . C T 151.9 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.59;MQ0=0;QD=21.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:15:180,15,0
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61 chr1 4438 . T C 90.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.849;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=13.69;MQ0=2;MQRankSum=2.700;QD=6.00;ReadPosRankSum=-2.855;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:10,5:15:12:118,12,0
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62 chr1 4555 . G A 51.74 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.51;MQ0=0;QD=17.25;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,3:3:6:79,6,0
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63 chr1 4733 . C G 135.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.22;MQ0=0;QD=22.51;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,6:6:12:163,12,0
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64 chr1 4879 . T C 114.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.81;MQ0=0;QD=19.01;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,6:6:12:142,12,0
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65 chr1 4945 . G A 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.415;DP=29;Dels=0.00;FS=3.123;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.25;MQ0=1;MQRankSum=3.132;QD=11.10;ReadPosRankSum=3.363;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:14,15:29:43:350,0,43
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66 chr1 4947 . C G 360.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.742;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.38;MQ0=1;MQRankSum=3.401;QD=11.64;ReadPosRankSum=3.360;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:16,15:31:40:389,0,40
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67 chr1 4961 . C T 42.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.427;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=25.65;MQ0=1;MQRankSum=-3.749;QD=0.99;ReadPosRankSum=-0.165;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:18,25:43:71:71,0,437
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68 chr1 4967 . T C 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.980;DP=41;Dels=0.00;FS=1.219;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=26.25;MQ0=1;MQRankSum=4.072;QD=10.09;ReadPosRankSum=-0.897;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:25,16:41:70:442,0,70
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69 chr1 4981 . A C 244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.018;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=6.8693;MLEAC=1;MLEAF=0.500;MQ=24.42;MQ0=1;MQRankSum=3.500;QD=6.80;ReadPosRankSum=-1.759;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:25,11:36:88:273,0,88
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70 chr1 4987 . T G 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.583;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=13.8254;MLEAC=1;MLEAF=0.500;MQ=24.42;MQ0=1;MQRankSum=-2.450;QD=1.66;ReadPosRankSum=1.983;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:21,15:36:88:88,0,296
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71 chr1 5059 . C G 146.84 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.14;MQ0=1;QD=18.35;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,8:8:18:175,18,0
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72 chr1 5110 . A G 94.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.328;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.75;MQ0=3;MQRankSum=-0.421;QD=4.51;ReadPosRankSum=-1.826;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:12,9:21:99:123,0,278
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73 chr1 5170 . A G 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.817;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=25.23;MQ0=2;MQRankSum=0.212;QD=3.65;ReadPosRankSum=0.533;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,7:15:83:83,0,127
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74 chr1 5171 . T G 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=26.11;MQ0=1;MQRankSum=0.212;QD=3.91;ReadPosRankSum=0.533;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,6:14:83:83,0,122
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75 chr1 5284 . A C 76.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.784;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=1.9827;MLEAC=1;MLEAF=0.500;MQ=34.72;MQ0=1;MQRankSum=-0.784;QD=3.49;ReadPosRankSum=-1.445;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:105,0,410
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76 chr1 5324 . C T 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.780;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.74;MQ0=3;MQRankSum=1.491;QD=10.44;ReadPosRankSum=-0.818;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:10,10:20:99:237,0,166
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77 chr1 5361 . A G 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.919;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=24.40;MQ0=2;MQRankSum=1.412;QD=11.41;ReadPosRankSum=0.688;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:9,14:24:44:302,0,44
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78 chr1 5557 . A G 298.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.74;MQ0=5;QD=18.67;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,16:16:30:327,30,0
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79 chr1 5648 . T C 59.28 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.66;MQ0=3;QD=6.59;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:1,8:9:9:87,9,0
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80 chr1 5834 . G T 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.714;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=3.3843;MLEAC=1;MLEAF=0.500;MQ=27.17;MQ0=1;MQRankSum=1.191;QD=0.93;ReadPosRankSum=0.714;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:15,2:17:44:44,0,279
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81 chr1 5889 . T G 147.1 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.488;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=21.23;MQ0=4;MQRankSum=-0.248;QD=8.17;ReadPosRankSum=-0.744;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:4,14:18:11:175,0,11
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82 chr1 5890 . T G 229.78 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=2;MLEAF=1.00;MQ=21.11;MQ0=4;QD=12.09;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,19:19:24:258,24,0
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83 chr1 5938 . C G 64.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.520;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=14.73;MQ0=10;MQRankSum=1.034;QD=3.08;ReadPosRankSum=0.597;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:15,6:21:69:93,0,69
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84 chr1 5968 . A T 115.9 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.07;MQ0=8;QD=7.24;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,16:16:15:144,15,0
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85 chr1 5974 . A G 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.818;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=18.51;MQ0=8;MQRankSum=0.296;QD=1.88;ReadPosRankSum=1.580;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:14,4:18:62:62,0,114
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86 chr1 6010 . A T 490.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.66;MQ0=2;QD=21.34;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,23:23:45:519,45,0
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87 chr1 6041 . T A 311.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=28.89;MQ0=0;QD=14.85;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,21:21:33:340,33,0
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88 chr1 6209 . A G 273.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.61;MQ0=6;QD=13.04;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,20:21:30:302,30,0
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89 chr1 6350 . T G 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=16.20;MQ0=21;MQRankSum=1.670;QD=2.93;ReadPosRankSum=-0.085;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:163,0,206
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90 chr1 6426 . T C 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=25.78;MQ0=2;MQRankSum=-1.099;QD=5.25;ReadPosRankSum=0.859;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:301,0,677
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91 chr1 6486 . A G 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=24.11;MQ0=16;MQRankSum=-0.330;QD=8.00;ReadPosRankSum=0.268;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:39,25:64:99:540,0,604
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92 chr1 6532 . C T 117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=53;Dels=0.00;FS=4.619;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=17.32;MQ0=28;MQRankSum=0.087;QD=2.22;ReadPosRankSum=-0.379;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:146,0,419
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93 chr1 6577 . G A 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.35;MQ0=17;MQRankSum=-1.883;QD=6.11;ReadPosRankSum=0.269;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,25:33:28:230,0,28
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94 chr1 6607 . T C 88.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.160;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=5.9778;MLEAC=1;MLEAF=0.500;MQ=18.87;MQ0=12;MQRankSum=-1.702;QD=2.28;ReadPosRankSum=0.321;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:117,0,385
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95 chr1 6609 . G T 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=5.9778;MLEAC=1;MLEAF=0.500;MQ=18.87;MQ0=12;MQRankSum=0.904;QD=2.30;ReadPosRankSum=-0.204;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:32,7:39:99:118,0,377
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96 chr1 6675 . G A 58.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.540;DP=52;Dels=0.00;FS=8.076;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=21.45;MQ0=15;MQRankSum=-1.788;QD=1.13;ReadPosRankSum=-0.973;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:36,16:52:87:87,0,729
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97 chr1 6691 . G T 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.208;DP=49;Dels=0.00;FS=8.321;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=21.34;MQ0=17;MQRankSum=-0.467;QD=0.71;ReadPosRankSum=-0.311;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:36,13:49:63:63,0,703
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98 chr1 6725 . G A 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.122;DP=26;Dels=0.00;FS=1.957;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=22.03;MQ0=9;MQRankSum=-0.927;QD=7.45;ReadPosRankSum=-0.146;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:13,13:26:99:222,0,183
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99 chr1 6752 . T C 113.9 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.88;MQ0=6;QD=10.35;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,11:11:15:142,15,0
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100 chr1 6942 . G C 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.400;DP=21;Dels=0.00;FS=13.222;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=17.08;MQ0=7;MQRankSum=0.267;QD=2.66;ReadPosRankSum=-1.067;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:14,7:21:84:84,0,137
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101 chr1 7107 . C T 262.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.283;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.07;MQ0=9;MQRankSum=1.189;QD=10.11;ReadPosRankSum=-1.302;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:7,19:26:6:290,6,0
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102 chr1 7384 . T G 58.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.259;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=10.91;MQ0=30;MQRankSum=0.259;QD=1.40;ReadPosRankSum=0.583;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:26,16:42:87:87,0,93
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103 chr1 8682 . T G 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.674;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=20.57;MQ0=23;MQRankSum=-1.898;QD=7.02;ReadPosRankSum=0.429;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:8,30:38:99:295,0,141
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104 chr1 8738 . A G 850.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.36;MQ0=29;QD=15.75;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,54:54:72:879,72,0
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105 chr1 8785 . C G 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.453;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.27;MQ0=40;MQRankSum=-2.450;QD=1.48;ReadPosRankSum=1.668;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:102,0,173
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106 chr1 8936 . C T 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.372;DP=47;Dels=0.00;FS=11.458;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.37;MQ0=14;MQRankSum=2.448;QD=5.61;ReadPosRankSum=1.430;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:35,12:47:99:292,0,700
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107 chr1 8946 . A G 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.028;DP=39;Dels=0.00;FS=15.108;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=30.14;MQ0=13;MQRankSum=1.417;QD=5.94;ReadPosRankSum=0.472;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:29,10:39:99:260,0,533
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108 chr1 9013 . A T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.159;DP=33;Dels=0.00;FS=3.522;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=12.84;MQ0=24;MQRankSum=0.729;QD=2.05;ReadPosRankSum=-0.361;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,9:33:96:96,0,100
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109 chr1 9080 . C T 61.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.633;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=17.47;MQ0=24;MQRankSum=-1.866;QD=1.82;ReadPosRankSum=0.633;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,13:34:90:90,0,190
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110 chr1 10305 . A G 786.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.23;MQ0=10;QD=23.84;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:6,27:33:63:815,63,0
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111 chr1 10540 . G C 306.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.965;DP=45;Dels=0.00;FS=17.175;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.78;MQ0=1;MQRankSum=-1.779;QD=6.82;ReadPosRankSum=2.279;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,13:45:99:335,0,1095
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112 chr1 10565 . T C 1007.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.695;DP=49;Dels=0.00;FS=38.615;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.02;MQ0=2;MQRankSum=0.662;QD=20.57;ReadPosRankSum=-2.211;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,31:49:99:1036,0,420
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113 chr1 10997 . G A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.243;DP=59;Dels=0.00;FS=1.096;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=27.99;MQ0=9;MQRankSum=0.204;QD=10.11;ReadPosRankSum=-0.961;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:625,0,593
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114 chr1 11025 . A G 281.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.321;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.25;MQ0=15;MQRankSum=-0.654;QD=4.94;ReadPosRankSum=1.721;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:37,20:57:99:310,0,779
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115 chr1 11026 . C T 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.001;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.25;MQ0=15;MQRankSum=-0.814;QD=4.84;ReadPosRankSum=1.694;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:37,20:57:99:304,0,778
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|
116 chr1 11155 . G T 882.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=2.9841;MLEAC=2;MLEAF=1.00;MQ=25.38;MQ0=8;QD=22.07;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,40:40:84:911,84,0
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|
117 chr1 11199 . G A 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.053;DP=54;Dels=0.00;FS=15.978;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.97;MQ0=5;MQRankSum=-2.335;QD=4.79;ReadPosRankSum=2.164;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:287,0,1004
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|
118 chr1 11255 . A G 80.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=45;Dels=0.00;FS=8.137;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=44.39;MQ0=0;MQRankSum=-1.761;QD=1.79;ReadPosRankSum=-2.826;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:35,10:45:99:109,0,1164
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119 chr1 11591 . G A 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.305;DP=31;Dels=0.00;FS=8.096;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.67;MQ0=1;MQRankSum=-3.119;QD=4.96;ReadPosRankSum=-1.665;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,9:31:99:182,0,762
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120 chr1 11716 . T C 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.463;DP=25;Dels=0.00;FS=10.193;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.67;MQ0=0;MQRankSum=-0.962;QD=0.60;ReadPosRankSum=-2.049;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,3:25:43:43,0,741
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121 chr1 11719 . A G 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.798;DP=25;Dels=0.00;FS=10.193;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.67;MQ0=0;MQRankSum=-1.213;QD=0.48;ReadPosRankSum=-2.132;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,3:25:40:40,0,773
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122 chr1 11750 . A T 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.197;DP=39;Dels=0.00;FS=9.839;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.68;MQ0=1;MQRankSum=-4.052;QD=2.58;ReadPosRankSum=-2.335;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,10:39:99:129,0,976
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123 chr1 11773 . T C 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.068;DP=49;Dels=0.00;FS=8.883;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=43.29;MQ0=1;MQRankSum=-5.316;QD=5.40;ReadPosRankSum=-0.400;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:33,16:49:99:293,0,1185
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124 chr1 11891 . A T 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.171;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=46.82;MQ0=0;MQRankSum=-3.709;QD=8.61;ReadPosRankSum=-0.055;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,18:47:99:433,0,1013
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125 chr1 11902 . A T 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.656;DP=42;Dels=0.00;FS=1.270;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=46.98;MQ0=0;MQRankSum=-3.019;QD=7.21;ReadPosRankSum=-0.525;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:331,0,973
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126 chr1 11906 . C T 303.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.095;DP=41;Dels=0.00;FS=2.845;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.51;MQ0=0;MQRankSum=-2.883;QD=7.41;ReadPosRankSum=-1.096;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:332,0,920
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|
127 chr1 11911 . C T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.998;DP=38;Dels=0.00;FS=3.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.65;MQ0=0;MQRankSum=-2.124;QD=4.81;ReadPosRankSum=0.193;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,11:38:99:211,0,908
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128 chr1 11921 . A T 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.641;DP=38;Dels=0.00;FS=5.870;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.80;MQ0=0;MQRankSum=-1.608;QD=3.52;ReadPosRankSum=0.348;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,10:38:99:162,0,926
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129 chr1 11929 . A G 112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.970;DP=36;Dels=0.00;FS=9.839;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.95;MQ0=0;MQRankSum=-1.465;QD=3.13;ReadPosRankSum=-0.171;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,8:36:99:141,0,932
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130 chr1 11994 . G A 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.393;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=38.03;MQ0=3;MQRankSum=-1.960;QD=1.98;ReadPosRankSum=0.635;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:38,12:50:99:127,0,1191
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131 chr1 12008 . C T 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.763;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=38.65;MQ0=3;MQRankSum=-3.004;QD=4.01;ReadPosRankSum=0.628;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:41,17:59:99:265,0,1308
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132 chr1 12023 . A G 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.395;DP=68;Dels=0.00;FS=3.645;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=41.63;MQ0=3;MQRankSum=-1.795;QD=7.56;ReadPosRankSum=-1.088;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:43,25:68:99:542,0,1441
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133 chr1 12050 . G C 807.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.379;DP=68;Dels=0.00;FS=5.033;HaplotypeScore=2.9268;MLEAC=1;MLEAF=0.500;MQ=45.50;MQ0=3;MQRankSum=-1.538;QD=11.88;ReadPosRankSum=-0.672;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:38,30:68:99:836,0,1326
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134 chr1 12090 . A G 888.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.008;DP=57;Dels=0.00;FS=2.245;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.95;MQ0=0;MQRankSum=-4.892;QD=15.59;ReadPosRankSum=1.141;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:917,0,995
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135 chr1 12162 . A T 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.357;DP=34;Dels=0.00;FS=3.329;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=48.98;MQ0=2;MQRankSum=-4.602;QD=6.88;ReadPosRankSum=-0.119;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:21,13:34:99:262,0,708
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136 chr1 12186 . G C 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.996;DP=38;Dels=0.00;FS=3.305;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.59;MQ0=2;MQRankSum=-3.949;QD=6.10;ReadPosRankSum=-1.854;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:25,13:38:99:260,0,884
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137 chr1 12195 . C G 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.111;DP=39;Dels=0.00;FS=1.488;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.51;MQ0=2;MQRankSum=-3.882;QD=4.64;ReadPosRankSum=-1.898;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,12:39:99:209,0,927
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138 chr1 12249 . G A 657.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.999;DP=56;Dels=0.00;FS=2.386;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.19;MQ0=0;MQRankSum=-5.596;QD=11.75;ReadPosRankSum=2.865;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:33,23:56:99:686,0,1109
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139 chr1 12250 . C A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.017;DP=56;Dels=0.00;FS=2.386;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.01;MQ0=0;MQRankSum=-5.563;QD=11.66;ReadPosRankSum=2.848;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:33,23:56:99:681,0,1094
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140 chr1 12252 . T C 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.084;DP=55;Dels=0.00;FS=2.426;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.00;MQ0=0;MQRankSum=-5.486;QD=12.00;ReadPosRankSum=2.722;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:688,0,1075
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141 chr1 12271 . A G 478.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.412;DP=47;Dels=0.00;FS=2.731;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.00;MQ0=0;MQRankSum=-5.395;QD=10.19;ReadPosRankSum=0.908;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:29,18:47:99:507,0,1022
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142 chr1 12273 . A G 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.777;DP=47;Dels=0.00;FS=2.731;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.00;MQ0=0;MQRankSum=-5.395;QD=10.00;ReadPosRankSum=0.711;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,18:47:99:498,0,1029
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143 chr1 12283 . T G 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=45;Dels=0.00;FS=6.601;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=48.83;MQ0=0;MQRankSum=-4.612;QD=8.97;ReadPosRankSum=-0.178;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:29,16:45:99:432,0,953
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144 chr1 12293 . G C 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.726;DP=43;Dels=0.00;FS=13.073;HaplotypeScore=1.8216;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=0;MQRankSum=-4.370;QD=9.81;ReadPosRankSum=-2.000;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:28,15:43:99:450,0,932
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145 chr1 12432 . C T 860.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.21;MQ0=0;QD=31.88;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,27:27:72:889,72,0
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146 chr1 12461 . A T 106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.557;DP=31;Dels=0.00;FS=6.929;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=43.06;MQ0=0;MQRankSum=-3.047;QD=3.44;ReadPosRankSum=2.099;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,8:31:99:135,0,662
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147 chr1 12610 . A C 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.083;DP=16;Dels=0.00;FS=2.796;HaplotypeScore=10.5708;MLEAC=1;MLEAF=0.500;MQ=55.68;MQ0=1;MQRankSum=1.371;QD=2.99;ReadPosRankSum=-2.526;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:13,3:16:76:76,0,324
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148 chr1 12640 . T G 605.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.9933;MLEAC=2;MLEAF=1.00;MQ=53.39;MQ0=1;QD=30.29;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,20:20:51:634,51,0
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149 chr1 12680 . A T 555.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.13;MQ0=1;QD=32.69;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,17:17:42:584,42,0
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150 chr1 12768 . A C 859.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.86;MQ0=0;QD=32.48;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:888,69,0
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151 chr1 12883 . G A 787.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.75;MQ0=0;QD=29.11;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:816,60,0
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152 chr1 12886 . G A 784.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.75;MQ0=0;QD=27.81;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:813,60,0
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153 chr1 12926 . T C 761.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.31;MQ0=0;QD=28.06;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:790,60,0
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|
154 chr1 12964 . G C 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.821;DP=38;Dels=0.00;FS=15.239;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=-3.703;QD=1.41;ReadPosRankSum=1.421;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,6:38:82:82,0,1161
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|
155 chr1 12993 . G T 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.014;DP=43;Dels=0.00;FS=25.224;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.59;MQ0=0;MQRankSum=-4.523;QD=5.20;ReadPosRankSum=-0.543;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,11:43:99:252,0,1151
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|
156 chr1 12994 . A T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.877;DP=43;Dels=0.00;FS=21.598;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.59;MQ0=0;MQRankSum=-4.528;QD=4.25;ReadPosRankSum=-1.193;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:33,10:43:99:211,0,1187
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|
157 chr1 13041 . G A 87.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.443;DP=33;Dels=0.00;FS=12.234;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=-3.337;QD=2.66;ReadPosRankSum=2.310;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,6:33:99:116,0,945
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|
158 chr1 13045 . G A 88.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;DP=32;Dels=0.00;FS=12.127;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.52;MQ0=0;MQRankSum=-3.307;QD=2.77;ReadPosRankSum=2.148;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,6:32:99:117,0,908
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|
159 chr1 13074 . C T 821.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.270;DP=27;Dels=0.00;FS=3.388;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.40;MQ0=0;MQRankSum=2.122;QD=30.44;ReadPosRankSum=0.424;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:3,24:27:32:850,32,0
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160 chr1 13123 . T A 1348.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.40;MQ0=0;QD=34.58;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1377,102,0
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|
161 chr1 13136 . C T 181.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.015;DP=41;Dels=0.00;FS=14.892;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.46;MQ0=0;MQRankSum=-1.074;QD=4.43;ReadPosRankSum=3.016;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,11:41:99:210,0,1033
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162 chr1 13137 . C T 1016.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.086;DP=42;Dels=0.00;FS=14.892;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.95;MQ0=0;MQRankSum=0.715;QD=24.21;ReadPosRankSum=-3.118;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:11,31:42:99:1045,0,215
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163 chr1 13270 . G A 1048.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.55;MQ0=3;QD=34.96;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,30:30:81:1077,81,0
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164 chr1 13273 . A T 280.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=30;Dels=0.00;FS=2.876;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.55;MQ0=3;MQRankSum=-3.741;QD=9.36;ReadPosRankSum=-1.280;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,10:30:99:309,0,598
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165 chr1 13280 . C A 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.606;DP=28;Dels=0.00;FS=2.840;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.14;MQ0=2;MQRankSum=-3.610;QD=8.85;ReadPosRankSum=-1.080;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,10:28:99:276,0,564
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166 chr1 13292 . C T 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.331;DP=29;Dels=0.00;FS=5.630;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.02;MQ0=2;MQRankSum=-3.138;QD=10.03;ReadPosRankSum=-0.276;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:319,0,601
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167 chr1 13308 . T G 280.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.223;DP=29;Dels=0.00;FS=2.733;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.10;MQ0=1;MQRankSum=-3.380;QD=9.68;ReadPosRankSum=3.332;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:309,0,644
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168 chr1 13344 . T C 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.118;DP=19;Dels=0.00;FS=23.096;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.08;MQ0=1;MQRankSum=-0.592;QD=1.94;ReadPosRankSum=-1.303;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:16,3:19:65:65,0,546
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169 chr1 13347 . A T 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.846;DP=21;Dels=0.00;FS=37.433;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.82;MQ0=1;MQRankSum=1.196;QD=5.47;ReadPosRankSum=-2.268;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:15,6:21:99:143,0,499
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170 chr1 13363 . G A 235.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.203;DP=17;Dels=0.00;FS=33.858;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.13;MQ0=0;MQRankSum=0.818;QD=13.87;ReadPosRankSum=0.337;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,8:17:99:264,0,308
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171 chr1 13378 . C G 198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=13;Dels=0.00;FS=19.956;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=50.71;MQ0=0;MQRankSum=0.529;QD=15.29;ReadPosRankSum=1.461;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:5,7:13:99:227,0,159
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172 chr1 13390 . T C 227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=13;Dels=0.00;FS=21.553;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.47;MQ0=0;MQRankSum=-0.212;QD=17.52;ReadPosRankSum=2.927;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:5,8:13:99:256,0,126
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173 chr1 13403 . G A 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.296;DP=10;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=-1.580;QD=21.18;ReadPosRankSum=2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:3,7:10:88:240,0,88
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174 chr1 13404 . T A 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;DP=10;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=0.895;QD=5.78;ReadPosRankSum=-2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,3:10:86:86,0,217
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175 chr1 13405 . A G 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;DP=10;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=1.580;QD=5.78;ReadPosRankSum=-2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,3:10:86:86,0,244
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176 chr1 13407 . C T 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.296;DP=10;Dels=0.00;FS=19.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=1.580;QD=5.48;ReadPosRankSum=-2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,3:10:83:83,0,214
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177 chr1 13424 . C A 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.550;DP=7;Dels=0.00;FS=15.441;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=54.99;MQ0=0;MQRankSum=-1.754;QD=13.25;ReadPosRankSum=-0.550;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:3,4:7:90:121,0,90
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178 chr1 13484 . T A 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=11;Dels=0.00;FS=6.264;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.36;MQ0=0;MQRankSum=-2.228;QD=9.07;ReadPosRankSum=-1.398;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,4:11:99:128,0,245
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179 chr1 13514 . C T 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.849;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.67;ReadPosRankSum=1.312;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:128,0,321
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180 chr1 13526 . C T 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.91;ReadPosRankSum=0.077;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:131,0,293
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181 chr1 13529 . T C 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.700;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.60;ReadPosRankSum=0.077;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:127,0,261
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182 chr1 13533 . A C 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.312;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.60;ReadPosRankSum=-0.849;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:127,0,316
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183 chr1 13543 . G T 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.200;DP=13;Dels=0.00;FS=16.782;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=54.07;MQ0=0;MQRankSum=0.377;QD=13.06;ReadPosRankSum=-2.777;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,6:13:99:198,0,209
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184 chr1 13601 . C T 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.355;DP=33;Dels=0.00;FS=6.893;HaplotypeScore=2.5316;MLEAC=1;MLEAF=0.500;MQ=51.49;MQ0=0;MQRankSum=-0.954;QD=18.30;ReadPosRankSum=1.732;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:12,20:33:99:632,0,392
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185 chr1 13654 . T G 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.876;DP=32;Dels=0.00;FS=2.000;HaplotypeScore=17.2143;MLEAC=1;MLEAF=0.500;MQ=44.78;MQ0=0;MQRankSum=-3.367;QD=6.71;ReadPosRankSum=0.876;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:243,0,696
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186 chr1 13805 . C T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.616;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=1.000;QD=13.95;ReadPosRankSum=1.081;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:712,0,955
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187 chr1 13962 . A T 843.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=56;Dels=0.00;FS=1.048;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.041;QD=15.07;ReadPosRankSum=0.567;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:872,0,1029
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188 chr1 14025 . A G 1167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=4.5620;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=0.490;QD=19.14;ReadPosRankSum=0.702;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,36:61:99:1196,0,669
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189 chr1 14039 . C T 781.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.305;DP=61;Dels=0.00;FS=1.002;HaplotypeScore=2.6609;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=0.839;QD=12.82;ReadPosRankSum=-1.116;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:35,26:61:99:810,0,1140
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190 chr1 14053 . A G 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.152;DP=61;Dels=0.00;FS=3.495;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=1.107;QD=16.44;ReadPosRankSum=1.469;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1031,0,874
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191 chr1 14525 . C T 1169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.228;DP=57;Dels=0.00;FS=7.529;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=-0.041;QD=20.52;ReadPosRankSum=0.447;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,34:57:99:1198,0,732
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192 chr1 14531 . A G 1030.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=54;Dels=0.00;FS=7.625;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=-0.153;QD=19.09;ReadPosRankSum=0.045;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:22,31:54:99:1059,0,726
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193 chr1 14540 . C T 1109.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.716;DP=56;Dels=0.00;FS=9.774;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=-0.899;QD=19.82;ReadPosRankSum=-0.716;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,33:56:99:1138,0,754
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194 chr1 14569 . T C 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=57;Dels=0.00;FS=3.724;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.646;QD=16.28;ReadPosRankSum=0.519;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:956,0,955
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|
195 chr1 14614 . T G 929.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.643;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-0.395;QD=17.88;ReadPosRankSum=-0.174;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,28:52:99:958,0,770
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196 chr1 14674 . G T 923.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.540;DP=54;Dels=0.00;FS=3.828;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=1.419;QD=17.11;ReadPosRankSum=1.228;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:27,27:54:99:952,0,875
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197 chr1 14720 . C A 2453.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.53;MQ0=0;QD=32.86;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2482,187,0
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198 chr1 14957 . C T 730.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.581;DP=43;Dels=0.00;FS=2.756;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.60;MQ0=1;MQRankSum=-0.253;QD=16.99;ReadPosRankSum=-0.758;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:759,0,646
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199 chr1 15110 . T A 822.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=65;Dels=0.00;FS=0.970;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=-0.569;QD=12.66;ReadPosRankSum=0.261;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:39,26:65:99:851,0,1349
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200 chr1 15135 . A G 1010.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.364;QD=16.04;ReadPosRankSum=-1.767;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:1039,0,1093
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201 chr1 15338 . C T 1812.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.74;MQ0=1;QD=24.29;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1841,138,0
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|
202 chr1 15597 . C A 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.595;DP=47;Dels=0.00;FS=6.639;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.617;QD=9.89;ReadPosRankSum=-0.797;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:31,16:47:99:493,0,1065
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203 chr1 15875 . A C 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.537;DP=42;Dels=0.00;FS=1.222;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=1;MQRankSum=-0.066;QD=12.90;ReadPosRankSum=1.064;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,19:42:99:570,0,798
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204 chr1 15977 . A T 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.672;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=53.37;MQ0=3;MQRankSum=-3.958;QD=12.64;ReadPosRankSum=-1.385;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,32:56:99:736,0,832
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205 chr1 16014 . C G 2424.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=10.8438;MLEAC=2;MLEAF=1.00;MQ=52.58;MQ0=3;QD=33.68;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,69:72:99:2453,187,0
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206 chr1 16017 . T G 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.483;DP=72;Dels=0.00;FS=1.018;HaplotypeScore=11.7597;MLEAC=1;MLEAF=0.500;MQ=52.21;MQ0=3;MQRankSum=-3.104;QD=11.80;ReadPosRankSum=-0.109;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:36,28:72:99:878,0,1143
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207 chr1 16621 . C T 1196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=65;Dels=0.00;FS=3.448;HaplotypeScore=2.7337;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.323;QD=18.41;ReadPosRankSum=-1.247;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:29,36:65:99:1225,0,946
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208 chr1 16671 . C T 1029.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.317;DP=52;Dels=0.00;FS=2.477;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.746;QD=19.80;ReadPosRankSum=0.075;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:21,31:52:99:1058,0,684
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209 chr1 16700 . C G 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.439;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=1.092;QD=18.80;ReadPosRankSum=-0.912;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:18,28:46:99:893,0,570
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210 chr1 16782 . C T 1114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.227;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9279;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=1.342;QD=17.69;ReadPosRankSum=-0.791;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:30,33:63:99:1143,0,988
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211 chr1 16844 . C A 2131.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.55;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2160,160,0
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212 chr1 16871 . T C 870.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.251;DP=59;Dels=0.00;FS=5.468;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.494;QD=14.76;ReadPosRankSum=-0.373;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:899,0,1075
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213 chr1 16912 . T A 808.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.631;DP=51;Dels=0.00;FS=7.963;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.556;QD=15.86;ReadPosRankSum=-1.724;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:837,0,878
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214 chr1 16926 . A G 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.660;DP=48;Dels=0.00;FS=6.044;HaplotypeScore=2.7745;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=0;MQRankSum=0.042;QD=14.35;ReadPosRankSum=-0.249;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:717,0,884
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215 chr1 17027 . T C 939.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.218;DP=65;Dels=0.00;FS=4.856;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.944;QD=14.46;ReadPosRankSum=-0.495;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:36,29:65:99:968,0,1247
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216 chr1 17241 . C G 946.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.434;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.811;QD=17.86;ReadPosRankSum=-0.258;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S190C|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_17170_17247),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:975,0,797
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217 chr1 17324 . T G 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.562;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.432;QD=18.63;ReadPosRankSum=0.875;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:20,26:46:99:885,0,675
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218 chr1 17567 . C T 1999.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.64;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2028,153,0
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219 chr1 17672 . A G 526.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.381;DP=37;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.326;QD=14.24;ReadPosRankSum=1.143;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:555,0,636
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220 chr1 17713 . A T 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.481;DP=51;Dels=0.00;FS=2.418;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.991;QD=15.64;ReadPosRankSum=-0.519;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:826,0,870
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221 chr1 17738 . G A 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.488;DP=56;Dels=0.00;FS=2.356;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.952;QD=12.19;ReadPosRankSum=0.820;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:711,0,1047
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222 chr1 17873 . G C 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.910;QD=21.06;ReadPosRankSum=0.728;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,29:46:99:997,0,530
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223 chr1 17905 . A G 1112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.065;DP=57;Dels=0.00;FS=2.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.659;QD=19.52;ReadPosRankSum=0.773;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,34:57:99:1141,0,733
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224 chr1 18041 . A G 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.146;DP=57;Dels=0.00;FS=2.316;HaplotypeScore=1.9991;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.610;QD=18.47;ReadPosRankSum=-0.569;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I221V|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_18036_18114) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1081,0,804
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225 chr1 18164 . G A 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.105;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=0.433;QD=11.99;ReadPosRankSum=-0.972;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,17:45:99:568,0,952
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226 chr1 18166 . T C 1777.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.02;MQ0=0;QD=28.69;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1806,135,0
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227 chr1 18454 . C T 729.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.010;DP=45;Dels=0.00;FS=1.130;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=0.329;QD=16.22;ReadPosRankSum=0.102;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T314M|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_18248_18565) GT:AD:DP:GQ:PL 0/1:22,23:45:99:758,0,703
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228 chr1 18478 . T C 502.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.230;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=2.9989;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=1.364;QD=13.59;ReadPosRankSum=1.242;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L322P|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_18248_18565) GT:AD:DP:GQ:PL 0/1:21,16:37:99:531,0,711
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229 chr1 18624 . T A 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=47;Dels=0.00;FS=4.335;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-0.140;QD=13.06;ReadPosRankSum=1.194;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:642,0,913
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230 chr1 19081 . C T 1168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.274;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.091;QD=22.92;ReadPosRankSum=-0.051;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A390|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_19027_19309) GT:AD:DP:GQ:PL 0/1:16,35:51:99:1197,0,486
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231 chr1 19138 . T C 862.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.496;DP=58;Dels=0.00;FS=5.223;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.717;QD=14.88;ReadPosRankSum=-0.655;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y409|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_19027_19309) GT:AD:DP:GQ:PL 0/1:31,27:58:99:891,0,1083
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232 chr1 19465 . T C 895.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.664;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.467;QD=16.00;ReadPosRankSum=-0.205;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,28:56:99:924,0,944
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233 chr1 19863 . T G 379.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.194;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=2.2772;MLEAC=1;MLEAF=0.500;MQ=60.50;MQ0=0;MQRankSum=-0.350;QD=8.83;ReadPosRankSum=-0.868;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,14:43:99:408,0,1042
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234 chr1 20158 . T C 868.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=0.686;QD=16.39;ReadPosRankSum=-0.668;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:897,0,842
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235 chr1 20454 . T C 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.377;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=-1.324;QD=15.62;ReadPosRankSum=0.255;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:700,0,709
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236 chr1 20566 . G T 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.182;DP=35;Dels=0.00;FS=3.009;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-1.275;QD=14.34;ReadPosRankSum=-2.633;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:530,0,669
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237 chr1 20614 . T C 732.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.266;DP=47;Dels=0.00;FS=1.121;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.223;QD=15.59;ReadPosRankSum=1.394;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:761,0,807
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238 chr1 20629 . A G 703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.400;DP=45;Dels=0.00;FS=1.143;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.830;QD=15.64;ReadPosRankSum=2.446;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:732,0,822
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239 chr1 20630 . A C 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.588;DP=43;Dels=0.00;FS=2.649;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.984;QD=16.60;ReadPosRankSum=1.956;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:742,0,712
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240 chr1 20726 . T G 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.220;DP=40;Dels=0.00;FS=1.408;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=0.190;QD=10.77;ReadPosRankSum=0.512;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:459,0,906
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241 chr1 20954 . G T 1159.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.044;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=1.566;QD=14.14;ReadPosRankSum=1.500;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:45,37:82:99:1188,0,1568
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242 chr1 21221 . G A 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.902;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.9994;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.356;QD=18.35;ReadPosRankSum=0.853;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L545|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_20985_21233) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1056,0,780
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243 chr1 21683 . C T 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.263;DP=55;Dels=0.00;FS=3.786;HaplotypeScore=2.9971;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=0.586;QD=14.07;ReadPosRankSum=-0.823;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,24:55:99:802,0,1087
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244 chr1 21687 . C T 1107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.157;DP=55;Dels=0.00;FS=1.070;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.182;QD=20.14;ReadPosRankSum=-0.026;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:1136,0,682
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245 chr1 21744 . A G 953.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.008;DP=57;Dels=0.00;FS=1.029;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.188;QD=16.73;ReadPosRankSum=-0.090;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,28:57:99:982,0,944
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246 chr1 21947 . T G 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.678;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=0.907;QD=12.46;ReadPosRankSum=-0.326;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:701,0,1131
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247 chr1 22299 . T C 948.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.094;DP=48;Dels=0.00;FS=6.116;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.826;QD=19.77;ReadPosRankSum=0.324;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A649|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_22000_23367) GT:AD:DP:GQ:PL 0/1:20,28:48:99:977,0,660
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248 chr1 22327 . T G 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.293;DP=45;Dels=0.00;FS=4.865;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.767;QD=21.53;ReadPosRankSum=-0.059;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S659A|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_22000_23367) GT:AD:DP:GQ:PL 0/1:17,28:45:99:997,0,550
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249 chr1 23334 . T G 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.500;DP=39;Dels=0.00;FS=2.875;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=0;MQRankSum=0.928;QD=12.87;ReadPosRankSum=-0.871;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A994|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_22000_23367) GT:AD:DP:GQ:PL 0/1:23,16:39:99:530,0,737
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250 chr1 23394 . A T 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.494;DP=52;Dels=0.00;FS=2.388;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.57;MQ0=0;MQRankSum=1.410;QD=16.90;ReadPosRankSum=0.531;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,27:52:99:907,0,841
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251 chr1 23447 . T A 768.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.205;DP=47;Dels=0.00;FS=1.119;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.054;QD=16.36;ReadPosRankSum=0.484;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,27:47:99:797,0,690
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252 chr1 23455 . T G 867.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.768;DP=47;Dels=0.00;FS=2.552;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=0.646;QD=18.46;ReadPosRankSum=-0.821;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:896,0,614
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253 chr1 23515 . G A,T 1409.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=59.35;MQ0=0;QD=32.03;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/2:0,23,21:44:99:1623,749,680,874,0,814
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254 chr1 23725 . G A 705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.981;DP=42;Dels=0.00;FS=6.684;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.428;QD=16.80;ReadPosRankSum=1.384;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:734,0,720
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255 chr1 23982 . C T 1069.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.194;DP=55;Dels=0.00;FS=2.640;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-1.005;QD=19.45;ReadPosRankSum=0.885;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,33:55:99:1098,0,682
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256 chr1 24069 . T A 743.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.713;DP=48;Dels=0.00;FS=8.862;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.89;MQ0=1;MQRankSum=0.330;QD=15.50;ReadPosRankSum=0.713;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:772,0,789
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257 chr1 24151 . A G 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.694;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=1;MQRankSum=0.785;QD=17.06;ReadPosRankSum=1.854;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1021|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_24104_24302) GT:AD:DP:GQ:PL 0/1:21,25:46:99:813,0,677
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258 chr1 24389 . C A 840.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.481;DP=48;Dels=0.00;FS=6.267;HaplotypeScore=27.9952;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=1;MQRankSum=0.567;QD=17.52;ReadPosRankSum=-0.546;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:869,0,711
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259 chr1 24436 . T C 934.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.691;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=1;MQRankSum=-1.964;QD=18.33;ReadPosRankSum=-0.577;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S1080|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_24411_24543) GT:AD:DP:GQ:PL 0/1:23,28:51:99:963,0,687
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260 chr1 24548 . G A 983.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.321;DP=46;Dels=0.00;FS=6.474;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=1.411;QD=21.39;ReadPosRankSum=1.479;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,29:46:99:1012,0,541
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261 chr1 24661 . C G 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.236;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9945;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-1.176;QD=13.44;ReadPosRankSum=1.960;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:687,0,875
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262 chr1 24708 . A T 506.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.037;DP=43;Dels=0.00;FS=1.164;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=57.71;MQ0=0;MQRankSum=-1.588;QD=11.79;ReadPosRankSum=-0.529;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:535,0,872
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263 chr1 24751 . C T 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.197;DP=50;Dels=0.00;FS=8.018;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-1.278;QD=12.94;ReadPosRankSum=-1.022;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:675,0,1009
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264 chr1 24820 . T A 1119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.600;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.461;QD=18.66;ReadPosRankSum=1.129;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,33:60:99:1148,0,824
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265 chr1 24862 . T C 689.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.409;DP=51;Dels=0.00;FS=13.641;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.789;QD=13.52;ReadPosRankSum=-0.238;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:718,0,995
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266 chr1 24930 . T C 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.762;DP=52;Dels=0.00;FS=27.617;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.560;QD=15.23;ReadPosRankSum=0.248;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:820,0,960
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267 chr1 25113 . T A 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;DP=40;Dels=0.00;FS=16.130;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=-0.639;QD=18.64;ReadPosRankSum=1.998;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,22:40:99:774,0,623
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268 chr1 25137 . G A 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.063;DP=36;Dels=0.00;FS=9.728;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=0.665;QD=17.66;ReadPosRankSum=-0.317;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,19:36:99:664,0,574
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269 chr1 25267 . A G 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.616;DP=44;Dels=0.00;FS=1.192;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.877;QD=18.93;ReadPosRankSum=-2.014;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:861,0,649
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270 chr1 25375 . A G 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.023;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=1.8311;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.084;QD=16.13;ReadPosRankSum=0.311;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:980,0,985
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271 chr1 25379 . A G 975.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.312;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.8311;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.716;QD=17.74;ReadPosRankSum=0.093;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:1004,0,818
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272 chr1 25601 . A G 966.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.979;DP=59;Dels=0.00;FS=7.277;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.584;QD=16.39;ReadPosRankSum=1.281;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:995,0,972
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273 chr1 25654 . G T 2337.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.57;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2366,175,0
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274 chr1 25678 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.915;DP=47;Dels=0.00;FS=2.654;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.653;QD=11.34;ReadPosRankSum=0.875;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1175|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_25668_25963) GT:AD:DP:GQ:PL 0/1:30,17:47:99:561,0,1005
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275 chr1 25747 . G A 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.324;DP=43;Dels=0.00;FS=7.186;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=0.246;QD=9.48;ReadPosRankSum=1.361;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S1198|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_25668_25963) GT:AD:DP:GQ:PL 0/1:29,14:43:99:436,0,1051
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276 chr1 25763 . G C 482.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.339;DP=44;Dels=0.00;FS=9.359;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.817;QD=10.97;ReadPosRankSum=-1.570;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Cta|V1204L|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_25668_25963) GT:AD:DP:GQ:PL 0/1:27,16:44:99:511,0,956
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277 chr1 26086 . G T 2202.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=3.4093;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.67;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2231,169,0
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278 chr1 26087 . A G 947.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DP=54;Dels=0.00;FS=1.059;HaplotypeScore=2.6207;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.099;QD=17.55;ReadPosRankSum=1.238;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,28:54:99:976,0,871
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279 chr1 26119 . G T 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.766;DP=55;Dels=0.00;FS=2.268;HaplotypeScore=2.9962;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.557;QD=16.52;ReadPosRankSum=-1.540;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:937,0,919
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280 chr1 26334 . G A 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.965;DP=50;Dels=0.00;FS=1.280;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=0;MQRankSum=-0.080;QD=6.24;ReadPosRankSum=3.146;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:38,12:50:99:340,0,1268
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281 chr1 26660 . T C 1722.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=38.42;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1751,129,0
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282 chr1 26702 . A T 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.942;DP=54;Dels=0.00;FS=10.090;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.192;QD=12.53;ReadPosRankSum=0.052;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:705,0,1095
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283 chr1 26910 . T G 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.210;DP=49;Dels=0.00;FS=1.167;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.332;QD=17.36;ReadPosRankSum=-0.491;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S1297A|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_26832_27933) GT:AD:DP:GQ:PL 0/1:23,26:49:99:879,0,760
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284 chr1 27095 . A T 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.581;DP=41;Dels=0.00;FS=4.926;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.784;QD=21.90;ReadPosRankSum=-0.151;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccT|P1358|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_26832_27933) GT:AD:DP:GQ:PL 0/1:14,27:41:99:926,0,391
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285 chr1 27394 . A G 928.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.355;DP=53;Dels=0.00;FS=5.960;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=1.100;QD=17.52;ReadPosRankSum=-0.809;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N1458S|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_26832_27933) GT:AD:DP:GQ:PL 0/1:21,32:53:99:957,0,694
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286 chr1 27940 . G T 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=2.7336;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=-0.545;QD=15.06;ReadPosRankSum=-0.078;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:781,0,874
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287 chr1 28249 . T G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.064;DP=41;Dels=0.00;FS=1.216;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.088;QD=19.41;ReadPosRankSum=0.696;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,23:41:99:824,0,613
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288 chr1 28269 . C T 816.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.304;DP=43;Dels=0.00;FS=2.755;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.609;QD=18.99;ReadPosRankSum=-1.031;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,26:43:99:845,0,552
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289 chr1 28430 . T C 718.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=51;Dels=0.00;FS=1.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.035;QD=14.09;ReadPosRankSum=-0.123;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:747,0,985
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290 chr1 28468 . T C 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.009;DP=55;Dels=0.00;FS=3.953;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=1;MQRankSum=0.650;QD=15.50;ReadPosRankSum=0.419;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,25:55:99:881,0,955
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291 chr1 28487 . T G 2391.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=59.01;MQ0=1;QD=33.84;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2420,178,0
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292 chr1 28990 . G T 1008.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.224;DP=58;Dels=0.00;FS=16.948;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.031;QD=17.39;ReadPosRankSum=0.202;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,29:58:99:1037,0,1003
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293 chr1 29042 . A C 1081.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.258;DP=57;Dels=0.00;FS=5.341;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.937;QD=18.98;ReadPosRankSum=1.049;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1110,0,905
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294 chr1 29090 . G T 1219.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.457;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.506;QD=23.46;ReadPosRankSum=-0.248;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:16,36:52:99:1248,0,498
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295 chr1 29155 . C T 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.754;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.513;QD=18.08;ReadPosRankSum=-0.050;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:914,0,699
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296 chr1 29212 . T C 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.539;DP=59;Dels=0.00;FS=2.209;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.359;QD=15.64;ReadPosRankSum=-2.011;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,28:59:99:951,0,1091
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297 chr1 29443 . T C 394.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.937;DP=47;Dels=0.00;FS=7.013;HaplotypeScore=2.8089;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=0.184;QD=8.40;ReadPosRankSum=0.033;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:423,0,970
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298 chr1 29543 . G C 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.839;DP=52;Dels=0.00;FS=2.441;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=2;MQRankSum=-0.700;QD=11.09;ReadPosRankSum=0.260;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:605,0,1005
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299 chr1 29549 . T A 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.246;DP=50;Dels=0.00;FS=4.262;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=2;MQRankSum=0.096;QD=11.00;ReadPosRankSum=0.607;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:578,0,972
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300 chr1 29794 . C G 717.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.493;DP=51;Dels=0.00;FS=4.035;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=0.447;QD=14.07;ReadPosRankSum=-0.865;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:746,0,926
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301 chr1 30062 . C G 1055.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.890;DP=56;Dels=0.00;FS=2.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=0.330;QD=18.85;ReadPosRankSum=0.725;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,31:56:99:1084,0,794
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302 chr1 30283 . A G 1779.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.20;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1808,135,0
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303 chr1 30505 . C T 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.057;DP=59;Dels=0.00;FS=3.878;HaplotypeScore=2.5980;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.388;QD=14.98;ReadPosRankSum=0.358;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T1668|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_30414_30776) GT:AD:DP:GQ:PL 0/1:32,27:59:99:912,0,1076
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304 chr1 30578 . A G 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.114;DP=59;Dels=0.00;FS=5.208;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-0.220;QD=16.66;ReadPosRankSum=0.523;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S1693G|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_30414_30776) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1011,0,918
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305 chr1 30610 . G A 853.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.888;DP=63;Dels=0.00;FS=2.122;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.012;QD=13.55;ReadPosRankSum=0.709;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S1703|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_30414_30776) GT:AD:DP:GQ:PL 0/1:33,30:63:99:882,0,1106
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306 chr1 30810 . T G 634.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.517;DP=52;Dels=0.00;FS=1.095;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=-0.743;QD=12.21;ReadPosRankSum=-0.141;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,20:52:99:663,0,1056
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307 chr1 30850 . G A 1094.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.596;DP=56;Dels=0.00;FS=1.064;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=0.864;QD=19.55;ReadPosRankSum=1.099;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,34:56:99:1123,0,720
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308 chr1 30887 . A C 998.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.265;DP=59;Dels=0.00;FS=7.277;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=0.841;QD=16.93;ReadPosRankSum=0.720;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1027,0,969
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309 chr1 30927 . C G 905.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.191;DP=49;Dels=0.00;FS=8.536;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=2.040;QD=18.49;ReadPosRankSum=1.296;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:934,0,707
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310 chr1 31004 . G T 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.387;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=1.766;QD=15.64;ReadPosRankSum=1.054;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:951,0,1000
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311 chr1 31025 . A C 964.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;DP=59;Dels=0.00;FS=5.136;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.371;QD=16.35;ReadPosRankSum=-0.205;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:993,0,950
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312 chr1 31036 . T G 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.630;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.81;MQ0=0;MQRankSum=0.950;QD=16.34;ReadPosRankSum=-0.770;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:829,0,810
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313 chr1 31213 . A G 898.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.198;DP=51;Dels=0.00;FS=3.933;HaplotypeScore=24.9899;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.293;QD=17.62;ReadPosRankSum=-0.311;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:927,0,826
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314 chr1 31497 . G A 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.007;DP=35;Dels=0.00;FS=4.982;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.347;QD=16.14;ReadPosRankSum=-0.479;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:593,0,535
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315 chr1 31537 . T A 1517.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.30;MQ0=0;QD=32.76;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1546,114,0
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316 chr1 31710 . G T 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.314;DP=41;Dels=0.00;FS=6.637;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.013;QD=13.19;ReadPosRankSum=0.876;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:569,0,741
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317 chr1 31712 . G A 1534.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=32.25;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1563,120,0
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318 chr1 31714 . A G 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.219;DP=40;Dels=0.00;FS=4.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.163;QD=15.17;ReadPosRankSum=1.165;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:635,0,705
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319 chr1 31754 . A T 662.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.308;DP=45;Dels=0.00;FS=1.145;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-1.058;QD=14.73;ReadPosRankSum=0.102;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:691,0,823
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320 chr1 31917 . G A 1231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.294;DP=60;Dels=0.00;FS=3.613;HaplotypeScore=1.9981;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.430;QD=20.53;ReadPosRankSum=0.174;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,36:60:99:1260,0,770
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321 chr1 31921 . G A 1051.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.128;DP=55;Dels=0.00;FS=1.022;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.561;QD=19.12;ReadPosRankSum=0.691;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1080,0,742
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322 chr1 32111 . A G 903.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.352;DP=49;Dels=0.00;FS=2.410;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.156;QD=18.44;ReadPosRankSum=0.211;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:932,0,729
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323 chr1 32214 . G A 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.166;DP=48;Dels=0.00;FS=6.054;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=1;MQRankSum=-0.118;QD=14.31;ReadPosRankSum=1.123;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:715,0,905
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324 chr1 32230 . T C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.182;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=2;MQRankSum=-0.176;QD=15.49;ReadPosRankSum=-1.233;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:710,0,732
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325 chr1 32312 . A T 916.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.306;DP=57;Dels=0.00;FS=7.278;HaplotypeScore=0.9159;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=1;MQRankSum=0.485;QD=16.08;ReadPosRankSum=-0.978;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,31:57:99:945,0,894
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326 chr1 32410 . A G 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.180;DP=58;Dels=0.00;FS=7.306;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-0.539;QD=13.43;ReadPosRankSum=-1.008;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:807,0,1109
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327 chr1 32760 . G T 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=55;Dels=0.00;FS=1.075;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-0.396;QD=15.74;ReadPosRankSum=0.648;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:894,0,892
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328 chr1 32761 . T G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.076;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=1.577;QD=15.01;ReadPosRankSum=1.274;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:824,0,925
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329 chr1 32762 . C T 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.506;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=0.151;QD=14.77;ReadPosRankSum=1.078;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:811,0,950
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330 chr1 32810 . T A 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.129;DP=44;Dels=0.00;FS=1.278;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=0;MQRankSum=0.481;QD=15.63;ReadPosRankSum=0.246;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:716,0,594
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331 chr1 32950 . A G 981.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.952;DP=47;Dels=0.00;FS=1.150;HaplotypeScore=2.4536;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.302;QD=20.89;ReadPosRankSum=-0.427;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V1779|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:1010,0,566
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332 chr1 33016 . T G 121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.707;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=1.8662;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=3;MQRankSum=-0.787;QD=2.54;ReadPosRankSum=-1.826;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccG|P1801|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,11:48:99:150,0,1307
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333 chr1 33031 . G A 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.602;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=10.1485;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=3;MQRankSum=0.261;QD=2.75;ReadPosRankSum=0.239;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q1806|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,13:56:99:182,0,1518
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334 chr1 33037 . T C 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.294;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=22.7136;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=3;MQRankSum=1.518;QD=11.25;ReadPosRankSum=0.008;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1808|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,22:59:99:692,0,1127
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335 chr1 33046 . T A 286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.993;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=13.5584;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=3;MQRankSum=-1.164;QD=4.86;ReadPosRankSum=0.237;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctA|L1811|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,17:59:99:315,0,1459
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336 chr1 33129 . A T 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.957;DP=65;Dels=0.00;FS=13.555;HaplotypeScore=1.6006;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=2.016;QD=6.77;ReadPosRankSum=-0.990;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K1839I|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,18:65:99:468,0,1588
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337 chr1 33136 . T A 417.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.123;DP=61;Dels=0.00;FS=16.845;HaplotypeScore=2.3893;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=2.025;QD=6.85;ReadPosRankSum=-1.090;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V1841|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,16:61:99:446,0,1486
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338 chr1 33139 . G T 370.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.245;DP=57;Dels=0.00;FS=11.731;HaplotypeScore=5.2554;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=1.441;QD=6.50;ReadPosRankSum=-1.169;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P1842|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,15:57:99:399,0,1431
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339 chr1 33146 . A C 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.634;DP=65;Dels=0.00;FS=13.675;HaplotypeScore=4.3887;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=0.261;QD=6.46;ReadPosRankSum=-1.112;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R1845|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:448,0,1646
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340 chr1 33199 . G A 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.004;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-0.694;QD=8.54;ReadPosRankSum=0.743;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V1862|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,21:72:99:643,0,1752
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341 chr1 33262 . G A 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.499;DP=78;Dels=0.00;FS=3.343;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-1.196;QD=7.68;ReadPosRankSum=-0.514;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G1883|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:54,24:78:99:627,0,1895
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342 chr1 33289 . A G 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=77;Dels=0.00;FS=6.644;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=1.605;QD=8.93;ReadPosRankSum=2.083;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S1892|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,25:77:99:716,0,1845
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343 chr1 33320 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.221;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-0.494;QD=8.34;ReadPosRankSum=0.778;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L1903|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,24:75:99:654,0,1810
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344 chr1 33322 . A G 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.707;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=0.160;QD=7.88;ReadPosRankSum=0.267;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L1903|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,23:74:99:611,0,1773
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345 chr1 33328 . C T 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.812;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=0.608;QD=8.90;ReadPosRankSum=-0.662;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L1905|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,26:76:99:705,0,1756
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346 chr1 33511 . T C 699.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.801;DP=90;Dels=0.00;FS=0.000;HaplotypeScore=28.0954;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-1.180;QD=7.78;ReadPosRankSum=-0.255;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:63,27:90:99:728,0,2042
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347 chr1 33518 . T A 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.325;DP=89;Dels=0.00;FS=0.876;HaplotypeScore=29.8838;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.272;QD=8.12;ReadPosRankSum=-1.798;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:62,27:89:99:751,0,2141
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348 chr1 33534 . A T 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.111;DP=82;Dels=0.00;FS=1.081;HaplotypeScore=4.6992;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.708;QD=3.67;ReadPosRankSum=0.006;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:66,16:82:99:329,0,2363
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349 chr1 33542 . A G 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.564;DP=84;Dels=0.00;FS=2.421;HaplotypeScore=3.3981;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-2.159;QD=3.43;ReadPosRankSum=-0.427;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:68,16:84:99:316,0,2385
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350 chr1 33544 . T C 222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.216;DP=85;Dels=0.00;FS=5.901;HaplotypeScore=2.3989;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=-2.519;QD=2.62;ReadPosRankSum=0.156;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:70,15:85:99:251,0,2424
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351 chr1 33549 . T C 271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.895;DP=85;Dels=0.00;FS=5.608;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=-0.928;QD=3.20;ReadPosRankSum=-0.983;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:68,17:85:99:300,0,2403
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352 chr1 33583 . A G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.860;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=2.8316;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=0.183;QD=6.04;ReadPosRankSum=-0.048;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:75,25:100:99:632,0,2624
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353 chr1 33591 . T G 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.288;DP=102;Dels=0.00;FS=0.000;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.576;QD=6.44;ReadPosRankSum=0.766;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:75,27:102:99:685,0,2559
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354 chr1 33634 . G T 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.830;DP=92;Dels=0.00;FS=2.888;HaplotypeScore=4.3078;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.309;QD=10.87;ReadPosRankSum=0.228;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:59,33:92:99:1028,0,2053
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355 chr1 33635 . T A 979.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.233;DP=93;Dels=0.00;FS=2.888;HaplotypeScore=4.3078;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.261;QD=10.54;ReadPosRankSum=0.285;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:60,33:93:99:1008,0,2023
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356 chr1 33648 . T C 1214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.582;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=29.5675;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.076;QD=12.40;ReadPosRankSum=-1.008;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:58,40:98:99:1243,0,1959
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357 chr1 33649 . T C 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.519;DP=97;Dels=0.00;FS=0.836;HaplotypeScore=29.5675;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-0.096;QD=8.31;ReadPosRankSum=3.319;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:67,29:97:99:834,0,2354
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358 chr1 33669 . A G 1169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.973;DP=93;Dels=0.00;FS=2.768;HaplotypeScore=17.9952;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.606;QD=12.58;ReadPosRankSum=0.465;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:55,38:93:99:1198,0,1907
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359 chr1 33692 . G A 1122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.680;DP=95;Dels=0.00;FS=8.628;HaplotypeScore=1.7719;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.994;QD=11.82;ReadPosRankSum=1.470;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:57,38:95:99:1151,0,1994
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360 chr1 33756 . T A 1044.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.209;DP=101;Dels=0.00;FS=21.595;HaplotypeScore=25.9789;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.917;QD=10.34;ReadPosRankSum=-0.467;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:66,35:101:99:1073,0,2323
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361 chr1 33765 . T C 2096.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.987;DP=97;Dels=0.00;FS=2.797;HaplotypeScore=26.9788;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=-0.109;QD=21.62;ReadPosRankSum=-1.754;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:35,62:97:99:2125,0,1120
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362 chr1 33783 . C A 3600.77 . AC=2;AF=1.00;AN=2;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=35.83;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,91:91:99:3629,274,0
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363 chr1 33800 . T C 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.274;DP=84;Dels=0.00;FS=1.935;HaplotypeScore=2.8243;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-2.651;QD=8.32;ReadPosRankSum=0.264;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:59,25:84:99:727,0,2083
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364 chr1 33805 . A G 2115.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.718;DP=85;Dels=0.00;FS=0.901;HaplotypeScore=2.8243;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=0;MQRankSum=4.074;QD=24.89;ReadPosRankSum=-0.738;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,60:85:99:2144,0,700
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365 chr1 33816 . T G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;DP=74;Dels=0.00;FS=2.126;HaplotypeScore=26.8598;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=-5.767;QD=8.16;ReadPosRankSum=0.084;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:53,21:74:99:632,0,1874
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366 chr1 33817 . C T 1791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.176;DP=75;Dels=0.00;FS=2.086;HaplotypeScore=25.9931;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-1.936;QD=23.89;ReadPosRankSum=-0.278;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,51:75:99:1820,0,743
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367 chr1 33825 . C G 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.639;DP=73;Dels=0.00;FS=2.189;HaplotypeScore=66.4539;MLEAC=1;MLEAF=0.500;MQ=57.65;MQ0=0;MQRankSum=-6.355;QD=8.34;ReadPosRankSum=-0.152;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:52,21:73:99:637,0,1756
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368 chr1 33827 . A G 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.248;DP=73;Dels=0.00;FS=3.559;HaplotypeScore=65.4541;MLEAC=1;MLEAF=0.500;MQ=57.65;MQ0=0;MQRankSum=-6.574;QD=8.26;ReadPosRankSum=-0.262;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:52,21:73:99:631,0,1850
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369 chr1 33850 . G A 967.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=85;Dels=0.00;FS=5.848;HaplotypeScore=20.9875;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=-4.789;QD=11.39;ReadPosRankSum=-1.730;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:54,31:85:99:996,0,1874
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370 chr1 33851 . C T 972.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.361;DP=85;Dels=0.00;FS=5.930;HaplotypeScore=20.9875;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=-5.199;QD=11.44;ReadPosRankSum=-1.593;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:54,31:85:99:1001,0,1842
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371 chr1 33860 . A T 1131.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.167;DP=94;Dels=0.00;FS=0.798;HaplotypeScore=46.8065;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=2.315;QD=12.04;ReadPosRankSum=-0.705;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:56,38:94:99:1160,0,1948
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372 chr1 33863 . A G 705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.497;DP=93;Dels=0.00;FS=0.897;HaplotypeScore=49.5927;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=2.899;QD=7.59;ReadPosRankSum=-0.568;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:68,25:93:99:734,0,2127
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373 chr1 33867 . T C 877.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.479;DP=88;Dels=0.00;FS=5.938;HaplotypeScore=51.2136;MLEAC=1;MLEAF=0.500;MQ=58.15;MQ0=0;MQRankSum=-2.770;QD=9.97;ReadPosRankSum=1.358;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:59,29:88:99:906,0,2073
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374 chr1 33870 . A T 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.369;DP=86;Dels=0.00;FS=6.242;HaplotypeScore=47.2312;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-3.848;QD=9.56;ReadPosRankSum=2.170;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:58,28:86:99:850,0,1959
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375 chr1 33871 . G C 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.345;DP=86;Dels=0.00;FS=7.832;HaplotypeScore=48.2298;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-3.203;QD=10.01;ReadPosRankSum=2.382;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:58,28:86:99:889,0,1966
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376 chr1 33872 . A T 861.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.005;DP=86;Dels=0.00;FS=5.975;HaplotypeScore=48.2298;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-2.211;QD=10.02;ReadPosRankSum=2.503;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:57,29:86:99:890,0,1958
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377 chr1 33881 . T C 2424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.386;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=26.4025;MLEAC=1;MLEAF=0.500;MQ=58.35;MQ0=0;MQRankSum=-0.490;QD=25.80;ReadPosRankSum=1.236;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,70:94:99:2453,0,686
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378 chr1 33890 . C T 1338.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.822;DP=97;Dels=0.00;FS=16.850;HaplotypeScore=21.9948;MLEAC=1;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=-2.421;QD=13.80;ReadPosRankSum=1.464;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:56,41:97:99:1367,0,1887
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379 chr1 33916 . A T 1213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.196;DP=82;Dels=0.00;FS=19.829;HaplotypeScore=1.8110;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.075;QD=14.80;ReadPosRankSum=1.230;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:45,37:82:99:1242,0,1531
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380 chr1 33954 . T A 3289.77 . AC=2;AF=1.00;AN=2;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=2;MLEAF=1.00;MQ=59.22;MQ0=0;QD=34.54;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,83:83:99:3318,250,0
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381 chr1 33959 . A T 872.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.821;DP=80;Dels=0.00;FS=8.032;HaplotypeScore=19.9908;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-1.205;QD=10.91;ReadPosRankSum=-0.277;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:52,28:80:99:901,0,1837
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382 chr1 33967 . G T 568.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.284;DP=83;Dels=0.00;FS=3.410;HaplotypeScore=22.8560;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.531;QD=6.85;ReadPosRankSum=0.160;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:61,22:83:99:597,0,2149
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383 chr1 33970 . T C 759.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.516;DP=83;Dels=0.00;FS=4.648;HaplotypeScore=21.8565;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-0.792;QD=9.15;ReadPosRankSum=-1.739;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:56,26:83:99:788,0,1880
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384 chr1 33978 . T C 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.466;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=0;MQRankSum=-1.032;QD=8.11;ReadPosRankSum=-1.314;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,23:81:99:685,0,2028
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385 chr1 33982 . G T 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.029;DP=77;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.12;MQ0=0;MQRankSum=-3.048;QD=7.57;ReadPosRankSum=-1.195;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,21:77:99:611,0,1932
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386 chr1 34048 . T C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.934;DP=83;Dels=0.00;FS=3.608;HaplotypeScore=36.7760;MLEAC=1;MLEAF=0.500;MQ=55.89;MQ0=1;MQRankSum=2.374;QD=5.44;ReadPosRankSum=1.714;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,20:83:99:480,0,2239
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387 chr1 34056 . A T 1152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.173;DP=83;Dels=0.00;FS=11.444;HaplotypeScore=20.9499;MLEAC=1;MLEAF=0.500;MQ=55.66;MQ0=1;MQRankSum=-5.405;QD=13.89;ReadPosRankSum=-2.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,36:83:99:1181,0,1566
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388 chr1 34066 . T C 1342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.343;DP=87;Dels=0.00;FS=8.990;HaplotypeScore=6.9949;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=2;MQRankSum=-5.146;QD=15.43;ReadPosRankSum=-0.920;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,40:87:99:1371,0,1526
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389 chr1 34080 . G A 227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.370;DP=97;Dels=0.00;FS=6.820;HaplotypeScore=18.9960;MLEAC=1;MLEAF=0.500;MQ=55.90;MQ0=2;MQRankSum=-2.713;QD=2.35;ReadPosRankSum=-0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,13:97:99:256,0,2928
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390 chr1 34081 . A G 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.776;DP=97;Dels=0.00;FS=1.486;HaplotypeScore=18.9960;MLEAC=1;MLEAF=0.500;MQ=55.90;MQ0=2;MQRankSum=-3.102;QD=0.20;ReadPosRankSum=1.722;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,8:97:48:48,0,3121
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391 chr1 34096 . C A 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.605;DP=104;Dels=0.00;FS=0.000;HaplotypeScore=13.7725;MLEAC=1;MLEAF=0.500;MQ=56.47;MQ0=1;MQRankSum=0.463;QD=5.36;ReadPosRankSum=3.585;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,22:104:99:586,0,2872
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392 chr1 34098 . A G 884.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.749;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=13.7725;MLEAC=1;MLEAF=0.500;MQ=56.44;MQ0=1;MQRankSum=-3.070;QD=8.59;ReadPosRankSum=3.187;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,31:103:99:913,0,2440
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393 chr1 34099 . T A 3974.77 . AC=2;AF=1.00;AN=2;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=13.7725;MLEAC=2;MLEAF=1.00;MQ=56.44;MQ0=1;QD=32.71;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,103:103:99:4003,298,0
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394 chr1 34115 . C T 508.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.165;DP=117;Dels=0.00;FS=2.007;HaplotypeScore=38.4977;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=1;MQRankSum=0.701;QD=4.35;ReadPosRankSum=0.440;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,22:117:99:537,0,3369
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395 chr1 34126 . A G 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.205;DP=133;Dels=0.00;FS=3.779;HaplotypeScore=3.5158;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=1;MQRankSum=4.108;QD=6.87;ReadPosRankSum=-0.606;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,34:133:99:942,0,3399
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396 chr1 34143 . T C 1202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.256;DP=120;Dels=0.00;FS=6.188;HaplotypeScore=2.5772;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=1;MQRankSum=1.550;QD=10.02;ReadPosRankSum=-0.532;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,40:120:99:1231,0,2753
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|
397 chr1 34161 . C T 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.244;DP=113;Dels=0.00;FS=0.978;HaplotypeScore=2.7868;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=1;MQRankSum=-0.596;QD=3.30;ReadPosRankSum=1.772;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,18:113:99:401,0,3276
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|
398 chr1 34191 . A G 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.445;DP=45;Dels=0.00;FS=9.532;HaplotypeScore=1.6553;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=0.990;QD=18.35;ReadPosRankSum=1.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,24:45:99:854,0,672
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|
399 chr1 34210 . A G 912.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.402;DP=49;Dels=0.00;FS=6.502;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.291;QD=18.63;ReadPosRankSum=0.372;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:941,0,668
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|
|
400 chr1 34256 . A T 558.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.236;DP=36;Dels=0.00;FS=2.987;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.317;QD=15.52;ReadPosRankSum=1.743;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,17:36:99:587,0,649
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|
401 chr1 34258 . C T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.342;DP=33;Dels=0.00;FS=3.093;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=0.991;QD=16.78;ReadPosRankSum=1.567;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,17:33:99:582,0,541
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|
402 chr1 34267 . C T 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.031;DP=43;Dels=0.00;FS=1.232;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=0.832;QD=12.16;ReadPosRankSum=0.186;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,17:43:99:551,0,893
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|
403 chr1 34273 . T C 987.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.491;DP=50;Dels=0.00;FS=4.059;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-1.867;QD=19.76;ReadPosRankSum=0.865;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:1016,0,658
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404 chr1 34278 . G C 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.618;DP=51;Dels=0.00;FS=4.059;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.998;QD=12.47;ReadPosRankSum=-1.360;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:664,0,1003
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405 chr1 34304 . G A 1178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.270;DP=62;Dels=0.00;FS=23.390;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=1.136;QD=19.01;ReadPosRankSum=0.511;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,35:62:99:1207,0,837
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406 chr1 34343 . C T 1038.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.620;DP=52;Dels=0.00;FS=19.687;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.695;QD=19.98;ReadPosRankSum=-1.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1067,0,693
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407 chr1 34344 . A G 2050.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=29.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2079,154,0
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|
408 chr1 34345 . A G 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.875;DP=53;Dels=0.00;FS=19.902;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-0.803;QD=12.77;ReadPosRankSum=1.742;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:705,0,1098
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409 chr1 34354 . G A 952.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.085;DP=50;Dels=0.00;FS=11.083;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=-1.241;QD=19.06;ReadPosRankSum=-1.182;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:981,0,660
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410 chr1 34385 . T G 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.698;DP=63;Dels=0.00;FS=57.702;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=48.13;MQ0=0;MQRankSum=-5.740;QD=12.35;ReadPosRankSum=-2.289;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:806,0,989
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411 chr1 34399 . A G 370.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.428;DP=48;Dels=0.00;FS=35.938;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=50.85;MQ0=0;MQRankSum=-4.904;QD=7.72;ReadPosRankSum=0.742;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,17:48:99:399,0,977
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412 chr1 34401 . G A 369.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.406;DP=47;Dels=0.00;FS=33.249;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=50.64;MQ0=0;MQRankSum=-4.904;QD=7.87;ReadPosRankSum=3.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,17:47:99:398,0,951
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413 chr1 34402 . C T 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.992;DP=48;Dels=0.00;FS=36.487;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=50.85;MQ0=0;MQRankSum=-4.958;QD=7.66;ReadPosRankSum=2.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,17:48:99:396,0,1008
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414 chr1 34406 . A C 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.650;DP=49;Dels=0.00;FS=17.048;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=-4.478;QD=1.51;ReadPosRankSum=2.915;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,10:49:99:102,0,1316
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415 chr1 34420 . C A 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.268;DP=45;Dels=0.00;FS=27.476;HaplotypeScore=2.6635;MLEAC=1;MLEAF=0.500;MQ=52.05;MQ0=0;MQRankSum=-4.989;QD=5.57;ReadPosRankSum=4.621;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:279,0,1055
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416 chr1 34423 . G C 249.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.758;DP=45;Dels=0.00;FS=27.476;HaplotypeScore=2.6635;MLEAC=1;MLEAF=0.500;MQ=52.05;MQ0=0;MQRankSum=-4.989;QD=5.55;ReadPosRankSum=4.989;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:278,0,1050
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417 chr1 34434 . C G 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.633;DP=29;Dels=0.00;FS=1.455;HaplotypeScore=1.6637;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.196;QD=12.99;ReadPosRankSum=0.065;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:15,14:29:99:405,0,509
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418 chr1 34498 . G A 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.733;DP=43;Dels=0.00;FS=5.601;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-0.273;QD=5.44;ReadPosRankSum=-0.129;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,10:43:99:262,0,1179
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419 chr1 34554 . A G 1556.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=0;QD=28.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1585,120,0
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420 chr1 34561 . G A 1507.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=59.53;MQ0=0;QD=28.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1536,123,0
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421 chr1 34587 . A G 554.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.670;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=1.339;QD=18.49;ReadPosRankSum=-1.256;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:583,0,433
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422 chr1 34649 . C T 1118.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.34;MQ0=0;QD=36.04;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1147,84,0
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423 chr1 34723 . C T 1680.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.32;MQ0=0;QD=32.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1709,132,0
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424 chr1 34750 . C T 820.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.677;DP=43;Dels=0.00;FS=6.795;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=55.31;MQ0=0;MQRankSum=0.628;QD=19.09;ReadPosRankSum=-1.096;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:849,0,524
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425 chr1 34774 . C A 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.360;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.29;MQ0=4;MQRankSum=-2.557;QD=0.57;ReadPosRankSum=-2.330;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,5:47:55:55,0,1310
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426 chr1 34784 . C T 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.845;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=47.92;MQ0=4;MQRankSum=-2.318;QD=1.69;ReadPosRankSum=-1.276;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,6:46:99:106,0,1235
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427 chr1 34787 . C T 84.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.498;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=47.62;MQ0=4;MQRankSum=-2.195;QD=1.88;ReadPosRankSum=-0.682;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,6:45:99:113,0,1162
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428 chr1 34789 . C G 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.047;DP=49;Dels=0.00;FS=1.637;HaplotypeScore=3.7163;MLEAC=1;MLEAF=0.500;MQ=47.34;MQ0=4;MQRankSum=-2.928;QD=2.06;ReadPosRankSum=-1.112;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,11:49:99:129,0,1309
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429 chr1 34798 . A G 471.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.482;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=4.7158;MLEAC=1;MLEAF=0.500;MQ=43.82;MQ0=4;MQRankSum=-3.693;QD=7.86;ReadPosRankSum=-1.219;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,18:60:99:500,0,1302
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430 chr1 34809 . A C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.319;DP=57;Dels=0.00;FS=2.399;HaplotypeScore=9.9935;MLEAC=1;MLEAF=0.500;MQ=43.70;MQ0=4;MQRankSum=-4.370;QD=11.56;ReadPosRankSum=-0.063;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,27:57:99:687,0,973
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431 chr1 34810 . A T 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.662;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=9.9935;MLEAC=1;MLEAF=0.500;MQ=43.70;MQ0=4;MQRankSum=-3.916;QD=8.31;ReadPosRankSum=1.249;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,18:57:99:502,0,1179
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432 chr1 34837 . G A 96.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.873;DP=54;Dels=0.00;FS=3.624;HaplotypeScore=73.4163;MLEAC=1;MLEAF=0.500;MQ=45.81;MQ0=4;MQRankSum=-0.811;QD=1.79;ReadPosRankSum=1.678;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,10:54:99:125,0,1456
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433 chr1 34841 . G A 106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.447;DP=52;Dels=0.00;FS=1.656;HaplotypeScore=90.4049;MLEAC=1;MLEAF=0.500;MQ=45.54;MQ0=4;MQRankSum=-0.555;QD=2.05;ReadPosRankSum=2.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,10:52:99:135,0,1269
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434 chr1 34842 . A G 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-3.032;DP=49;Dels=0.00;FS=4.664;HaplotypeScore=91.4038;MLEAC=1;MLEAF=0.500;MQ=45.63;MQ0=4;MQRankSum=1.770;QD=0.55;ReadPosRankSum=-3.277;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,6:49:55:55,0,1172
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435 chr1 34864 . A G 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.198;DP=48;Dels=0.00;FS=9.092;HaplotypeScore=49.3566;MLEAC=1;MLEAF=0.500;MQ=53.31;MQ0=1;MQRankSum=-4.082;QD=7.35;ReadPosRankSum=3.873;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,14:48:99:381,0,1135
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436 chr1 34865 . A G 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.419;DP=48;Dels=0.00;FS=19.848;HaplotypeScore=56.3327;MLEAC=1;MLEAF=0.500;MQ=53.31;MQ0=1;MQRankSum=-2.525;QD=1.75;ReadPosRankSum=3.123;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,7:48:99:112,0,1393
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437 chr1 34879 . G C 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=71;Dels=0.04;FS=44.625;HaplotypeScore=41.5658;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=4;MQRankSum=-6.053;QD=8.41;ReadPosRankSum=-2.378;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,27:68:99:625,0,1412
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438 chr1 34886 . A T 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.471;DP=74;Dels=0.00;FS=13.029;HaplotypeScore=24.3736;MLEAC=1;MLEAF=0.500;MQ=48.85;MQ0=4;MQRankSum=-3.738;QD=0.75;ReadPosRankSum=-2.040;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,10:74:84:84,0,2145
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439 chr1 34898 . G A 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.605;DP=77;Dels=0.00;FS=42.789;HaplotypeScore=2.7797;MLEAC=1;MLEAF=0.500;MQ=48.86;MQ0=4;MQRankSum=-5.924;QD=7.45;ReadPosRankSum=0.652;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,27:77:99:602,0,1708
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440 chr1 34918 . G A 1463.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.14;MQ0=1;QD=29.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1492,114,0
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441 chr1 34936 . A C 1246.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.631;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.68;MQ0=0;MQRankSum=-1.529;QD=26.64;ReadPosRankSum=1.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,33:34:78:1275,78,0
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442 chr1 34944 . G T 1292.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.41;MQ0=0;QD=31.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1321,99,0
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443 chr1 34949 . A T 1277.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.41;MQ0=0;QD=31.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1306,99,0
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444 chr1 34958 . G A 1117.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=7.7321;MLEAC=2;MLEAF=1.00;MQ=50.57;MQ0=0;QD=28.34;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1146,87,0
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445 chr1 34980 . A C 287.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.76;MQ0=0;QD=33.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:316,24,0
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446 chr1 34983 . A T 363.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.46;MQ0=0;QD=30.83;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:392,30,0
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447 chr1 34999 . C T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.241;DP=46;Dels=0.00;FS=5.844;HaplotypeScore=1.8318;MLEAC=1;MLEAF=0.500;MQ=50.81;MQ0=0;MQRankSum=-2.426;QD=3.97;ReadPosRankSum=-3.873;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,9:46:99:211,0,1278
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448 chr1 35001 . T C 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.443;DP=47;Dels=0.00;FS=8.113;HaplotypeScore=1.8318;MLEAC=1;MLEAF=0.500;MQ=50.71;MQ0=0;MQRankSum=-2.404;QD=4.29;ReadPosRankSum=-3.522;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,10:47:99:230,0,1358
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449 chr1 35012 . C T 3813.77 . AC=2;AF=1.00;AN=2;DP=121;Dels=0.00;FS=0.000;HaplotypeScore=1.9984;MLEAC=2;MLEAF=1.00;MQ=43.12;MQ0=18;QD=31.52;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,121:121:99:3842,307,0
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450 chr1 35021 . C A 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.012;DP=128;Dels=0.00;FS=17.106;HaplotypeScore=9.9826;MLEAC=1;MLEAF=0.500;MQ=43.09;MQ0=18;MQRankSum=-0.515;QD=0.24;ReadPosRankSum=2.376;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:118,10:128:59:59,0,3327
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451 chr1 35026 . C T 1359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.350;DP=127;Dels=0.00;FS=27.172;HaplotypeScore=10.7166;MLEAC=1;MLEAF=0.500;MQ=43.10;MQ0=18;MQRankSum=-7.635;QD=10.71;ReadPosRankSum=-3.755;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,50:127:99:1388,0,1991
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452 chr1 35045 . T C 238.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=133;Dels=0.00;FS=0.000;HaplotypeScore=40.6483;MLEAC=1;MLEAF=0.500;MQ=46.17;MQ0=16;MQRankSum=3.328;QD=1.80;ReadPosRankSum=-0.988;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:117,16:133:99:267,0,3398
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453 chr1 35046 . A G 1154.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.005;DP=127;Dels=0.00;FS=27.280;HaplotypeScore=39.9143;MLEAC=1;MLEAF=0.500;MQ=47.31;MQ0=14;MQRankSum=-8.458;QD=9.09;ReadPosRankSum=4.649;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:83,44:127:99:1183,0,2391
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454 chr1 35047 . T C 1481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.640;DP=126;Dels=0.00;FS=10.732;HaplotypeScore=40.9141;MLEAC=1;MLEAF=0.500;MQ=47.97;MQ0=14;MQRankSum=-8.951;QD=11.76;ReadPosRankSum=7.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,51:126:99:1510,0,2115
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455 chr1 35052 . A T 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.239;DP=120;Dels=0.00;FS=2.223;HaplotypeScore=77.1059;MLEAC=1;MLEAF=0.500;MQ=49.27;MQ0=9;MQRankSum=2.565;QD=2.49;ReadPosRankSum=-2.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:104,16:120:99:327,0,3293
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456 chr1 35056 . C T 4286.77 . AC=2;AF=1.00;AN=2;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=62.1757;MLEAC=2;MLEAF=1.00;MQ=50.09;MQ0=7;QD=31.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,120:120:99:4315,337,0
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457 chr1 35058 . C T 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.351;DP=119;Dels=0.00;FS=4.666;HaplotypeScore=52.1779;MLEAC=1;MLEAF=0.500;MQ=50.70;MQ0=5;MQRankSum=-5.373;QD=3.75;ReadPosRankSum=2.500;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,23:119:99:475,0,3197
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458 chr1 35060 . G A 79.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.055;DP=117;Dels=0.00;FS=17.881;HaplotypeScore=51.1782;MLEAC=1;MLEAF=0.500;MQ=51.17;MQ0=4;MQRankSum=-5.477;QD=0.68;ReadPosRankSum=3.813;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:103,14:117:99:108,0,3463
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459 chr1 35062 . G A 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.950;DP=113;Dels=0.00;FS=18.470;HaplotypeScore=57.1737;MLEAC=1;MLEAF=0.500;MQ=52.38;MQ0=0;MQRankSum=-8.371;QD=7.89;ReadPosRankSum=5.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,36:113:99:920,0,2624
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460 chr1 35075 . G C 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.602;DP=107;Dels=0.00;FS=5.257;HaplotypeScore=32.3401;MLEAC=1;MLEAF=0.500;MQ=53.81;MQ0=0;MQRankSum=-8.219;QD=7.81;ReadPosRankSum=1.447;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,33:107:99:864,0,2509
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461 chr1 35077 . C G 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.450;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=33.3400;MLEAC=1;MLEAF=0.500;MQ=53.72;MQ0=0;MQRankSum=-5.857;QD=2.21;ReadPosRankSum=0.993;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,14:107:99:265,0,2739
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462 chr1 35087 . C T 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.133;DP=97;Dels=0.00;FS=2.025;HaplotypeScore=16.1548;MLEAC=1;MLEAF=0.500;MQ=54.33;MQ0=0;MQRankSum=-7.328;QD=5.34;ReadPosRankSum=-2.579;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,24:97:99:546,0,2468
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463 chr1 35095 . C T 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.785;DP=88;Dels=0.00;FS=1.246;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=56.73;MQ0=0;MQRankSum=-5.345;QD=0.66;ReadPosRankSum=-2.995;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:76,11:88:86:86,0,2675
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464 chr1 35096 . A G 27.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.348;DP=88;Dels=0.00;FS=1.393;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=56.94;MQ0=0;MQRankSum=-5.134;QD=0.32;ReadPosRankSum=-2.860;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,10:88:56:56,0,2777
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465 chr1 35164 . T G 3737.77 . AC=2;AF=1.00;AN=2;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=115.8992;MLEAC=2;MLEAF=1.00;MQ=55.84;MQ0=0;QD=26.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,95:95:99:3766,283,0
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466 chr1 35172 . A C 1478.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.986;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=29.8173;MLEAC=1;MLEAF=0.500;MQ=54.75;MQ0=2;MQRankSum=2.017;QD=14.64;ReadPosRankSum=1.119;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,46:101:99:1507,0,1792
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467 chr1 35184 . C G 3588.77 . AC=2;AF=1.00;AN=2;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.10;MQ0=2;QD=33.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,97:97:99:3617,277,0
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468 chr1 35205 . G A 2760.77 . AC=2;AF=1.00;AN=2;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=2;MLEAF=1.00;MQ=50.07;MQ0=2;QD=34.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,80:80:99:2789,217,0
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469 chr1 35248 . T C 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.610;DP=59;Dels=0.00;FS=5.425;HaplotypeScore=11.8817;MLEAC=1;MLEAF=0.500;MQ=36.39;MQ0=4;MQRankSum=1.904;QD=4.39;ReadPosRankSum=-1.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,13:59:99:287,0,1045
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470 chr1 35251 . A G 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.617;DP=57;Dels=0.00;FS=6.294;HaplotypeScore=10.9876;MLEAC=1;MLEAF=0.500;MQ=36.08;MQ0=4;MQRankSum=-1.563;QD=8.49;ReadPosRankSum=2.153;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:512,0,755
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471 chr1 35260 . T G 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.080;DP=49;Dels=0.00;FS=2.866;HaplotypeScore=5.9548;MLEAC=1;MLEAF=0.500;MQ=32.62;MQ0=4;MQRankSum=-1.252;QD=6.97;ReadPosRankSum=2.493;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:370,0,613
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472 chr1 35264 . G A 863.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=5.9548;MLEAC=2;MLEAF=1.00;MQ=29.67;MQ0=4;QD=21.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,41:41:75:892,75,0
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473 chr1 35265 . C A 872.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=5.9548;MLEAC=2;MLEAF=1.00;MQ=30.23;MQ0=4;QD=20.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,41:41:75:901,75,0
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474 chr1 35283 . A G 1303.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=3.9990;MLEAC=2;MLEAF=1.00;MQ=35.84;MQ0=2;QD=24.60;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,52:53:99:1332,111,0
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475 chr1 35288 . G T 267.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.229;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=6.9868;MLEAC=1;MLEAF=0.500;MQ=37.11;MQ0=2;MQRankSum=-1.073;QD=4.96;ReadPosRankSum=2.419;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:296,0,926
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476 chr1 35292 . T C 1507.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.062;DP=60;Dels=0.00;FS=4.130;HaplotypeScore=6.9868;MLEAC=2;MLEAF=1.00;MQ=40.07;MQ0=2;MQRankSum=-0.557;QD=25.13;ReadPosRankSum=0.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,57:60:92:1536,92,0
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477 chr1 35316 . G A 2080.77 . AC=2;AF=1.00;AN=2;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=0.9734;MLEAC=2;MLEAF=1.00;MQ=43.24;MQ0=1;QD=31.06;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,67:67:99:2109,165,0
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478 chr1 35396 . A G 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.266;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=2.6626;MLEAC=1;MLEAF=0.500;MQ=54.52;MQ0=0;MQRankSum=3.180;QD=22.13;ReadPosRankSum=0.855;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,29:43:99:980,0,405
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479 chr1 35403 . C T 1648.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=1.6634;MLEAC=2;MLEAF=1.00;MQ=54.38;MQ0=0;QD=35.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1677,126,0
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480 chr1 35406 . T G 369.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=2.6632;MLEAC=1;MLEAF=0.500;MQ=54.09;MQ0=0;MQRankSum=-2.541;QD=9.24;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,13:40:99:398,0,951
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481 chr1 35445 . C T 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.615;DP=32;Dels=0.00;FS=3.211;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=45.27;MQ0=0;MQRankSum=2.394;QD=21.12;ReadPosRankSum=-0.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:12,20:32:99:704,0,324
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482 chr1 35483 . T A 221.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.021;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.95;MQ0=0;MQRankSum=-1.247;QD=7.15;ReadPosRankSum=-1.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,10:31:99:250,0,750
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483 chr1 35491 . G T 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.408;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=20.9946;MLEAC=1;MLEAF=0.500;MQ=48.70;MQ0=0;MQRankSum=1.222;QD=19.59;ReadPosRankSum=1.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:15,22:37:99:753,0,428
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484 chr1 35497 . G A 1437.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=20.9946;MLEAC=2;MLEAF=1.00;MQ=48.93;MQ0=0;QD=32.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1466,111,0
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485 chr1 35499 . A G 470.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.411;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=21.8612;MLEAC=1;MLEAF=0.500;MQ=48.22;MQ0=1;MQRankSum=-1.459;QD=11.77;ReadPosRankSum=-1.487;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,18:40:99:499,0,781
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486 chr1 35561 . A T 530.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.63;MQ0=0;QD=35.92;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:559,42,0
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487 chr1 35564 . T A 470.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.36;MQ0=0;QD=29.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:12:36:499,36,0
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488 chr1 35576 . G A 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.516;DP=32;Dels=0.00;FS=3.734;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=51.67;MQ0=1;MQRankSum=-4.149;QD=7.84;ReadPosRankSum=-4.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:279,0,688
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489 chr1 35588 . C T 342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.111;DP=38;Dels=0.00;FS=5.225;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=1;MQRankSum=-3.261;QD=9.02;ReadPosRankSum=-2.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:371,0,819
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490 chr1 35633 . G A 1506.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=53.32;MQ0=1;QD=27.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:1535,117,0
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491 chr1 35691 . T C 1735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.139;DP=81;Dels=0.00;FS=0.889;HaplotypeScore=1.7319;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=0.513;QD=21.43;ReadPosRankSum=0.601;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,51:81:99:1764,0,836
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492 chr1 35707 . C A 3162.77 . AC=2;AF=1.00;AN=2;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=2;MLEAF=1.00;MQ=58.97;MQ0=0;QD=32.53;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,82:82:99:3191,238,0
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493 chr1 35739 . G A 342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.072;DP=74;Dels=0.00;FS=17.134;HaplotypeScore=1.6483;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=-0.689;QD=4.63;ReadPosRankSum=-2.515;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,16:74:99:371,0,2031
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494 chr1 35804 . T C 667.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.427;DP=109;Dels=0.00;FS=5.672;HaplotypeScore=3.9987;MLEAC=1;MLEAF=0.500;MQ=53.96;MQ0=1;MQRankSum=-6.467;QD=6.13;ReadPosRankSum=0.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,28:109:99:696,0,2821
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495 chr1 35807 . A G 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.906;DP=108;Dels=0.00;FS=7.240;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=2;MQRankSum=-6.417;QD=6.27;ReadPosRankSum=0.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,28:108:99:705,0,2709
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496 chr1 35843 . A T 2756.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=56.90;MQ0=0;QD=30.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,72:72:99:2785,214,0
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497 chr1 35857 . C A 148.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.592;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=53.9074;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=0;MQRankSum=-0.442;QD=2.19;ReadPosRankSum=-1.176;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,10:68:99:177,0,1820
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498 chr1 35860 . A C 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.173;DP=74;Dels=0.00;FS=3.561;HaplotypeScore=73.8862;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=0;MQRankSum=0.722;QD=6.77;ReadPosRankSum=3.931;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,20:74:99:529,0,1811
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499 chr1 35870 . A T 2448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.943;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=27.0091;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=1;MQRankSum=2.228;QD=26.05;ReadPosRankSum=-0.574;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,72:94:99:2477,0,566
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500 chr1 35900 . T C 3238.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.355;DP=119;Dels=0.00;FS=8.381;HaplotypeScore=194.4919;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=3;MQRankSum=-1.040;QD=27.22;ReadPosRankSum=1.369;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,96:119:99:3267,0,489
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501 chr1 35951 . T A 1015.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.446;DP=127;Dels=0.00;FS=0.000;HaplotypeScore=1.7331;MLEAC=1;MLEAF=0.500;MQ=56.75;MQ0=2;MQRankSum=-0.149;QD=8.00;ReadPosRankSum=0.625;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,37:127:99:1044,0,2832
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502 chr1 35968 . C T 2056.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=50.3624;MLEAC=2;MLEAF=1.00;MQ=56.18;MQ0=0;QD=29.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,55:56:99:2085,162,0
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503 chr1 35979 . G A 85.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.196;DP=96;Dels=0.00;FS=17.564;HaplotypeScore=12.6997;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=2;MQRankSum=-1.392;QD=0.89;ReadPosRankSum=3.011;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,10:96:99:114,0,2869
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504 chr1 36004 . G A 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.254;DP=72;Dels=0.00;FS=9.104;HaplotypeScore=76.6328;MLEAC=1;MLEAF=0.500;MQ=56.83;MQ0=0;MQRankSum=-1.369;QD=0.25;ReadPosRankSum=-1.140;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:65,7:72:46:46,0,2207
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505 chr1 36045 . T C 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=132;Dels=0.00;FS=0.896;HaplotypeScore=43.4929;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-0.565;QD=3.33;ReadPosRankSum=1.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:110,22:132:99:468,0,3861
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506 chr1 36103 . G C 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.632;DP=141;Dels=0.00;FS=41.173;HaplotypeScore=7.9970;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=1.254;QD=0.83;ReadPosRankSum=2.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:126,15:141:99:145,0,4391
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507 chr1 36153 . G C 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.401;DP=89;Dels=0.00;FS=7.730;HaplotypeScore=3.8273;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.014;QD=6.33;ReadPosRankSum=1.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,21:89:99:592,0,2434
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508 chr1 36180 . T A 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.539;DP=100;Dels=0.00;FS=0.858;HaplotypeScore=3.7118;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.137;QD=7.78;ReadPosRankSum=0.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,29:100:99:806,0,2559
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509 chr1 36205 . C T 965.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.427;DP=124;Dels=0.00;FS=0.755;HaplotypeScore=17.7034;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=0.466;QD=7.79;ReadPosRankSum=-0.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,35:124:99:994,0,3181
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510 chr1 36213 . T C 194.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.280;DP=132;Dels=0.00;FS=2.347;HaplotypeScore=19.5352;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-0.237;QD=1.48;ReadPosRankSum=0.294;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:117,15:132:99:223,0,4265
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511 chr1 36259 . T C 887.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.248;DP=134;Dels=0.00;FS=3.770;HaplotypeScore=89.4890;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=-1.222;QD=6.63;ReadPosRankSum=-1.341;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,33:134:99:916,0,3559
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512 chr1 36261 . A G 780.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.776;DP=132;Dels=0.00;FS=2.746;HaplotypeScore=86.5740;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=0.433;QD=5.91;ReadPosRankSum=-0.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,32:132:99:809,0,3579
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513 chr1 36273 . T C 678.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.181;DP=118;Dels=0.00;FS=1.774;HaplotypeScore=117.6849;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.361;QD=5.75;ReadPosRankSum=-0.661;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,28:118:99:707,0,3229
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514 chr1 36286 . A T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.030;DP=98;Dels=0.00;FS=0.915;HaplotypeScore=132.2089;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=1;MQRankSum=2.210;QD=5.89;ReadPosRankSum=0.615;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,23:98:99:605,0,2724
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515 chr1 36287 . A T 2373.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.322;DP=96;Dels=0.00;FS=1.851;HaplotypeScore=132.2089;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=1;MQRankSum=0.853;QD=24.73;ReadPosRankSum=1.588;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,68:96:99:2402,0,835
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516 chr1 36289 . T A 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.239;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=83.8835;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=1;MQRankSum=2.678;QD=5.48;ReadPosRankSum=1.179;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,22:99:99:571,0,2798
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517 chr1 36290 . A T 2719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.543;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=84.8831;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=1;MQRankSum=-1.327;QD=27.20;ReadPosRankSum=-0.453;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,76:100:99:2748,0,648
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518 chr1 36320 . T A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.153;DP=92;Dels=0.00;FS=0.939;HaplotypeScore=45.5348;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=1;MQRankSum=-3.017;QD=6.49;ReadPosRankSum=0.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,23:92:99:625,0,2459
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519 chr1 36333 . G A 2428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.737;DP=96;Dels=0.00;FS=12.492;HaplotypeScore=24.9952;MLEAC=1;MLEAF=0.500;MQ=56.69;MQ0=1;MQRankSum=-3.960;QD=25.30;ReadPosRankSum=0.841;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,71:96:99:2457,0,747
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520 chr1 36341 . T C 895.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.506;DP=100;Dels=0.00;FS=14.157;HaplotypeScore=25.7839;MLEAC=1;MLEAF=0.500;MQ=56.08;MQ0=1;MQRankSum=-3.263;QD=8.96;ReadPosRankSum=0.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,30:100:99:924,0,2374
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521 chr1 36361 . G A 2302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.530;DP=91;Dels=0.00;FS=2.218;HaplotypeScore=4.6978;MLEAC=1;MLEAF=0.500;MQ=55.09;MQ0=1;MQRankSum=-4.586;QD=25.31;ReadPosRankSum=1.413;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,69:91:99:2331,0,612
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522 chr1 36362 . T G 3325.77 . AC=2;AF=1.00;AN=2;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=3.9091;MLEAC=2;MLEAF=1.00;MQ=54.92;MQ0=1;QD=32.06;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,88:88:99:3354,250,0
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523 chr1 36377 . A G 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.990;DP=102;Dels=0.00;FS=10.835;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.49;MQ0=0;MQRankSum=-5.406;QD=9.55;ReadPosRankSum=-0.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,34:102:99:1002,0,2367
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524 chr1 36383 . T C 997.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.211;DP=103;Dels=0.00;FS=9.011;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.87;MQ0=0;MQRankSum=-6.104;QD=9.69;ReadPosRankSum=-0.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,36:103:99:1026,0,2320
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525 chr1 36393 . G A 924.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.454;DP=108;Dels=0.00;FS=2.766;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=52.35;MQ0=0;MQRankSum=-6.108;QD=8.56;ReadPosRankSum=-0.505;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,38:108:99:953,0,2423
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526 chr1 36408 . C T 2376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=104;Dels=0.00;FS=4.359;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=51.96;MQ0=0;MQRankSum=-0.816;QD=22.85;ReadPosRankSum=-0.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,77:104:99:2405,0,763
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527 chr1 36427 . A T 616.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.872;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=3.8148;MLEAC=1;MLEAF=0.500;MQ=51.50;MQ0=0;MQRankSum=-6.246;QD=6.56;ReadPosRankSum=2.278;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,28:94:99:645,0,2385
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528 chr1 36447 . A T 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.515;DP=107;Dels=0.00;FS=0.770;HaplotypeScore=3.5157;MLEAC=1;MLEAF=0.500;MQ=51.35;MQ0=0;MQRankSum=-6.584;QD=7.45;ReadPosRankSum=-0.880;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,35:107:99:825,0,2544
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529 chr1 36455 . A C 803.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.393;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=26.1134;MLEAC=1;MLEAF=0.500;MQ=51.36;MQ0=0;MQRankSum=-6.423;QD=7.65;ReadPosRankSum=-1.462;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,36:105:99:832,0,2482
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530 chr1 36464 . A C 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.836;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=48.2350;MLEAC=1;MLEAF=0.500;MQ=51.21;MQ0=0;MQRankSum=-2.154;QD=5.85;ReadPosRankSum=1.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,23:98:99:602,0,2428
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531 chr1 36466 . C T 1703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.251;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=27.3765;MLEAC=1;MLEAF=0.500;MQ=51.39;MQ0=0;MQRankSum=-7.882;QD=17.75;ReadPosRankSum=-0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,59:96:99:1732,0,1115
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532 chr1 36483 . A G 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.080;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=51.61;MQ0=0;MQRankSum=-3.339;QD=5.65;ReadPosRankSum=0.429;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,21:91:99:542,0,2305
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533 chr1 36503 . T C 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.074;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=80.4897;MLEAC=1;MLEAF=0.500;MQ=50.33;MQ0=0;MQRankSum=-0.635;QD=0.59;ReadPosRankSum=3.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,9:86:79:79,0,2347
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534 chr1 36504 . T C 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.112;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=80.4897;MLEAC=1;MLEAF=0.500;MQ=50.57;MQ0=0;MQRankSum=-2.130;QD=5.11;ReadPosRankSum=5.608;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,19:88:99:478,0,2018
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535 chr1 36505 . T C 375.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.063;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=79.0748;MLEAC=1;MLEAF=0.500;MQ=50.57;MQ0=0;MQRankSum=-2.029;QD=4.27;ReadPosRankSum=5.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,17:88:99:404,0,2137
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536 chr1 36518 . A G 895.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.366;DP=101;Dels=0.00;FS=5.616;HaplotypeScore=12.9006;MLEAC=1;MLEAF=0.500;MQ=47.84;MQ0=0;MQRankSum=-1.467;QD=8.87;ReadPosRankSum=0.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,35:101:99:924,0,1480
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537 chr1 36532 . C G 269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.644;DP=115;Dels=0.00;FS=1.129;HaplotypeScore=33.9847;MLEAC=1;MLEAF=0.500;MQ=49.03;MQ0=0;MQRankSum=2.072;QD=2.35;ReadPosRankSum=-1.765;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,15:115:99:298,0,2777
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538 chr1 36538 . C T 1246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.600;DP=114;Dels=0.00;FS=3.778;HaplotypeScore=31.9878;MLEAC=1;MLEAF=0.500;MQ=49.12;MQ0=0;MQRankSum=-8.542;QD=10.94;ReadPosRankSum=0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,62:114:99:1275,0,1800
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539 chr1 36561 . C T 997.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=91;Dels=0.00;FS=7.684;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=0;MQRankSum=-6.542;QD=10.96;ReadPosRankSum=0.491;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,33:91:99:1026,0,2069
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540 chr1 36566 . G A 965.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.004;DP=95;Dels=0.00;FS=7.431;HaplotypeScore=17.9938;MLEAC=1;MLEAF=0.500;MQ=54.20;MQ0=0;MQRankSum=-6.234;QD=10.17;ReadPosRankSum=-0.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,33:95:99:994,0,2189
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541 chr1 36574 . G A 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.133;DP=93;Dels=0.00;FS=3.666;HaplotypeScore=36.9659;MLEAC=1;MLEAF=0.500;MQ=54.28;MQ0=0;MQRankSum=-1.444;QD=4.45;ReadPosRankSum=1.036;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,18:93:99:442,0,2629
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542 chr1 36578 . G A 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.154;DP=83;Dels=0.00;FS=3.342;HaplotypeScore=35.9664;MLEAC=1;MLEAF=0.500;MQ=54.25;MQ0=0;MQRankSum=-5.365;QD=8.58;ReadPosRankSum=0.452;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,25:83:99:740,0,2021
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543 chr1 36581 . A G 2449.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=35.9664;MLEAC=2;MLEAF=1.00;MQ=53.85;MQ0=0;QD=24.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2478,187,0
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544 chr1 36582 . G A 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.643;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=35.9664;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-1.757;QD=7.39;ReadPosRankSum=1.154;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,17:63:99:494,0,1649
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545 chr1 36587 . G A 559.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.268;DP=64;Dels=0.00;FS=1.061;HaplotypeScore=19.9719;MLEAC=1;MLEAF=0.500;MQ=53.79;MQ0=0;MQRankSum=-4.946;QD=8.75;ReadPosRankSum=-0.007;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,20:64:99:588,0,1587
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546 chr1 36594 . C T 1517.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.57;MQ0=0;QD=31.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1546,117,0
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547 chr1 36595 . A C 1513.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.66;MQ0=0;QD=24.96;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1542,120,0
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548 chr1 36601 . T C 1588.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.66;MQ0=0;QD=28.60;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1617,120,0
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549 chr1 36605 . C T 1541.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.66;MQ0=0;QD=34.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1570,117,0
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550 chr1 36616 . C T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.418;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.18;MQ0=0;MQRankSum=-5.166;QD=11.34;ReadPosRankSum=-0.538;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,15:38:99:459,0,805
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551 chr1 36621 . T C 459.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.251;DP=36;Dels=0.00;FS=1.421;HaplotypeScore=1.9985;MLEAC=1;MLEAF=0.500;MQ=56.02;MQ0=0;MQRankSum=-4.460;QD=12.77;ReadPosRankSum=-1.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:488,0,751
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552 chr1 36626 . C T 362.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.429;DP=67;Dels=0.00;FS=6.207;HaplotypeScore=1.9985;MLEAC=1;MLEAF=0.500;MQ=53.11;MQ0=0;MQRankSum=-2.986;QD=5.41;ReadPosRankSum=0.609;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,15:67:99:391,0,1838
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553 chr1 36630 . T C 2560.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=1.9985;MLEAC=2;MLEAF=1.00;MQ=53.65;MQ0=0;QD=32.76;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2589,196,0
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554 chr1 36644 . A G 2044.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.378;DP=77;Dels=0.00;FS=0.000;HaplotypeScore=14.7297;MLEAC=1;MLEAF=0.500;MQ=53.58;MQ0=0;MQRankSum=-4.784;QD=26.56;ReadPosRankSum=-3.027;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,59:77:99:2073,0,508
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555 chr1 36651 . C T 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.907;DP=75;Dels=0.00;FS=2.457;HaplotypeScore=29.6893;MLEAC=1;MLEAF=0.500;MQ=53.83;MQ0=0;MQRankSum=-2.272;QD=4.60;ReadPosRankSum=-2.563;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,15:75:99:373,0,2131
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556 chr1 36656 . T C 248.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.462;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=16.6941;MLEAC=1;MLEAF=0.500;MQ=54.41;MQ0=0;MQRankSum=-3.172;QD=3.11;ReadPosRankSum=2.792;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,14:80:99:277,0,2375
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557 chr1 36662 . A G 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.984;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=33.6895;MLEAC=1;MLEAF=0.500;MQ=55.48;MQ0=0;MQRankSum=-1.103;QD=5.30;ReadPosRankSum=-1.807;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,17:80:99:452,0,2194
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558 chr1 36667 . A G 1572.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.127;DP=88;Dels=0.00;FS=6.014;HaplotypeScore=19.7292;MLEAC=1;MLEAF=0.500;MQ=55.49;MQ0=0;MQRankSum=-3.331;QD=17.87;ReadPosRankSum=3.641;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,48:88:99:1601,0,1351
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559 chr1 36673 . G T 1522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.190;DP=87;Dels=0.00;FS=6.027;HaplotypeScore=50.6295;MLEAC=1;MLEAF=0.500;MQ=55.85;MQ0=0;MQRankSum=-3.286;QD=17.50;ReadPosRankSum=4.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,46:87:99:1551,0,1404
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560 chr1 36679 . G A,C 994.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.028;DP=83;Dels=0.00;FS=6.491;HaplotypeScore=3.6668;MLEAC=1,1;MLEAF=0.500,0.500;MQ=55.79;MQ0=0;MQRankSum=-3.906;QD=11.98;ReadPosRankSum=3.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:18,20,45:83:99:1681,965,1561,114,0,635
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561 chr1 36680 . G T 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.401;DP=83;Dels=0.00;FS=1.073;HaplotypeScore=37.6485;MLEAC=1;MLEAF=0.500;MQ=55.81;MQ0=0;MQRankSum=0.921;QD=6.54;ReadPosRankSum=1.102;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,20:83:99:571,0,2139
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562 chr1 36681 . C A 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.220;DP=83;Dels=0.00;FS=2.291;HaplotypeScore=37.6485;MLEAC=1;MLEAF=0.500;MQ=55.95;MQ0=0;MQRankSum=0.648;QD=6.82;ReadPosRankSum=0.977;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,21:83:99:594,0,2067
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563 chr1 36692 . C T 2055.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.272;DP=84;Dels=0.00;FS=1.085;HaplotypeScore=21.9809;MLEAC=1;MLEAF=0.500;MQ=56.56;MQ0=0;MQRankSum=-2.422;QD=24.47;ReadPosRankSum=2.614;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,63:83:99:2084,0,534
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564 chr1 36698 . C A 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.419;DP=83;Dels=0.00;FS=8.813;HaplotypeScore=18.7747;MLEAC=1;MLEAF=0.500;MQ=56.60;MQ0=0;MQRankSum=0.221;QD=9.43;ReadPosRankSum=1.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,26:83:99:811,0,1969
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565 chr1 36713 . G A 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.135;DP=86;Dels=0.00;FS=1.174;HaplotypeScore=17.5182;MLEAC=1;MLEAF=0.500;MQ=57.16;MQ0=0;MQRankSum=-5.106;QD=3.24;ReadPosRankSum=1.351;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,14:86:99:307,0,2592
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566 chr1 36714 . G A 1263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=86;Dels=0.00;FS=13.988;HaplotypeScore=17.5182;MLEAC=1;MLEAF=0.500;MQ=57.16;MQ0=0;MQRankSum=-2.103;QD=14.69;ReadPosRankSum=-0.913;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,39:86:99:1292,0,1579
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567 chr1 36726 . G A 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.723;DP=93;Dels=0.00;FS=12.102;HaplotypeScore=22.7149;MLEAC=1;MLEAF=0.500;MQ=57.37;MQ0=0;MQRankSum=2.213;QD=7.48;ReadPosRankSum=0.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,26:93:99:724,0,2287
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568 chr1 36731 . A G 2521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.037;DP=95;Dels=0.00;FS=2.183;HaplotypeScore=22.5037;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=0;MQRankSum=-1.447;QD=26.54;ReadPosRankSum=-2.098;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,76:95:99:2550,0,452
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569 chr1 36745 . C G 1591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.959;DP=97;Dels=0.00;FS=21.761;HaplotypeScore=2.1877;MLEAC=1;MLEAF=0.500;MQ=57.21;MQ0=0;MQRankSum=-3.929;QD=16.41;ReadPosRankSum=1.490;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,49:97:99:1620,0,1518
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570 chr1 36764 . T C 1128.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.112;DP=75;Dels=0.00;FS=17.360;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=-2.794;QD=15.05;ReadPosRankSum=4.475;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,34:75:99:1157,0,1382
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571 chr1 36765 . T G 1076.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.179;DP=75;Dels=0.00;FS=14.729;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=0;MQRankSum=-2.439;QD=14.36;ReadPosRankSum=4.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,33:75:99:1105,0,1430
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572 chr1 36767 . T C 1198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.723;DP=76;Dels=0.00;FS=14.305;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-2.429;QD=15.77;ReadPosRankSum=3.761;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,36:76:99:1227,0,1335
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573 chr1 36796 . G A 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.162;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=22.8300;MLEAC=1;MLEAF=0.500;MQ=55.32;MQ0=0;MQRankSum=-6.512;QD=3.92;ReadPosRankSum=0.721;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,23:100:99:420,0,2683
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574 chr1 36817 . A G 1277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.149;DP=101;Dels=0.00;FS=1.617;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=55.03;MQ0=0;MQRankSum=-2.941;QD=12.65;ReadPosRankSum=0.673;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,45:101:99:1306,0,1931
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575 chr1 36850 . G A 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=113;Dels=0.00;FS=1.797;HaplotypeScore=42.9345;MLEAC=1;MLEAF=0.500;MQ=56.24;MQ0=0;MQRankSum=2.503;QD=6.50;ReadPosRankSum=-0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,28:113:99:763,0,2839
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576 chr1 36857 . T C 462.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.537;DP=112;Dels=0.00;FS=6.385;HaplotypeScore=44.9514;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=0;MQRankSum=-0.969;QD=4.13;ReadPosRankSum=-0.119;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,21:112:99:491,0,3074
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577 chr1 36860 . T A 1910.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.351;DP=112;Dels=0.00;FS=10.516;HaplotypeScore=64.8364;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=0;MQRankSum=0.143;QD=17.06;ReadPosRankSum=-0.750;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,60:112:99:1939,0,1715
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578 chr1 36867 . T C 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.043;DP=115;Dels=0.00;FS=2.674;HaplotypeScore=43.9466;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=0.637;QD=7.66;ReadPosRankSum=-0.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,34:115:99:909,0,2706
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579 chr1 36869 . A G 1776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.227;DP=112;Dels=0.00;FS=8.872;HaplotypeScore=21.9682;MLEAC=1;MLEAF=0.500;MQ=57.28;MQ0=1;MQRankSum=0.192;QD=15.86;ReadPosRankSum=0.156;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,55:112:99:1805,0,1829
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580 chr1 36898 . T G 3694.77 . AC=2;AF=1.00;AN=2;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=58.61;MQ0=1;QD=33.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,99:99:99:3723,283,0
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581 chr1 36921 . G A 1095.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.776;DP=105;Dels=0.00;FS=1.642;HaplotypeScore=58.3901;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=1;MQRankSum=0.967;QD=10.44;ReadPosRankSum=0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,37:105:99:1124,0,2298
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582 chr1 36924 . T C 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.282;DP=104;Dels=0.01;FS=11.095;HaplotypeScore=64.0672;MLEAC=1;MLEAF=0.500;MQ=57.91;MQ0=1;MQRankSum=-0.152;QD=6.57;ReadPosRankSum=0.341;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:76,27:103:99:711,0,2625
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583 chr1 36928 . T A 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.431;DP=101;Dels=0.01;FS=13.977;HaplotypeScore=62.9043;MLEAC=1;MLEAF=0.500;MQ=57.71;MQ0=1;MQRankSum=-0.447;QD=6.57;ReadPosRankSum=0.382;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,26:100:99:692,0,2509
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584 chr1 36933 . A G 1741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.768;DP=98;Dels=0.00;FS=1.634;HaplotypeScore=39.9143;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=3.401;QD=17.77;ReadPosRankSum=-0.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,53:98:99:1770,0,1349
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585 chr1 36937 . C T 1282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.506;DP=96;Dels=0.00;FS=1.678;HaplotypeScore=21.5624;MLEAC=1;MLEAF=0.500;MQ=56.75;MQ0=1;MQRankSum=-2.005;QD=13.36;ReadPosRankSum=-0.139;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:54,42:96:99:1311,0,1753
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586 chr1 36951 . A G 3101.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.536;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=4.9494;MLEAC=2;MLEAF=1.00;MQ=54.16;MQ0=2;MQRankSum=1.691;QD=31.53;ReadPosRankSum=-1.402;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,85:86:99:3130,247,0
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587 chr1 36957 . A G 3098.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.648;DP=84;Dels=0.00;FS=0.000;HaplotypeScore=3.2851;MLEAC=2;MLEAF=1.00;MQ=53.34;MQ0=2;MQRankSum=1.690;QD=28.09;ReadPosRankSum=-1.605;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,83:84:99:3127,241,0
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588 chr1 36980 . G C 390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.637;DP=87;Dels=0.00;FS=5.532;HaplotypeScore=19.2784;MLEAC=1;MLEAF=0.500;MQ=50.04;MQ0=1;MQRankSum=-2.668;QD=4.49;ReadPosRankSum=1.236;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,17:87:99:419,0,2324
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589 chr1 36986 . G A,T 2608.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=1.692;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=1.6385;MLEAC=1,1;MLEAF=0.500,0.500;MQ=49.63;MQ0=1;MQRankSum=-0.418;QD=29.64;ReadPosRankSum=-1.015;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/2:1,37,50:88:99:2946,1693,1587,1253,0,1106
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590 chr1 36990 . C T 1065.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.356;DP=88;Dels=0.00;FS=11.050;HaplotypeScore=16.5790;MLEAC=1;MLEAF=0.500;MQ=49.22;MQ0=1;MQRankSum=-2.013;QD=12.11;ReadPosRankSum=-0.219;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:50,38:88:99:1094,0,1532
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591 chr1 37033 . C T 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=97;Dels=0.00;FS=29.507;HaplotypeScore=60.3467;MLEAC=1;MLEAF=0.500;MQ=44.66;MQ0=1;MQRankSum=1.751;QD=5.93;ReadPosRankSum=-1.433;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:74,23:97:99:603,0,2295
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592 chr1 37035 . G A 1683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.258;DP=95;Dels=0.00;FS=32.836;HaplotypeScore=60.3467;MLEAC=1;MLEAF=0.500;MQ=44.62;MQ0=1;MQRankSum=-1.237;QD=17.72;ReadPosRankSum=0.597;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:39,56:95:99:1712,0,1110
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593 chr1 37086 . T C 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=83;Dels=0.00;FS=8.748;HaplotypeScore=15.4050;MLEAC=1;MLEAF=0.500;MQ=40.57;MQ0=1;MQRankSum=0.495;QD=6.67;ReadPosRankSum=-0.464;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:60,23:83:99:582,0,1632
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594 chr1 37098 . G A 259.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.373;DP=78;Dels=0.00;FS=22.975;HaplotypeScore=17.1337;MLEAC=1;MLEAF=0.500;MQ=38.80;MQ0=1;MQRankSum=2.695;QD=3.33;ReadPosRankSum=0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:63,15:78:99:288,0,1577
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595 chr1 37106 . A C 1959.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.633;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=9.8922;MLEAC=2;MLEAF=1.00;MQ=38.34;MQ0=1;MQRankSum=-0.247;QD=27.60;ReadPosRankSum=0.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),START_GAINED(LOW||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:1,70:71:99:1988,143,0
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596 chr1 37110 . G A 255.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.299;DP=70;Dels=0.00;FS=20.054;HaplotypeScore=6.6058;MLEAC=1;MLEAF=0.500;MQ=37.34;MQ0=1;MQRankSum=2.417;QD=3.65;ReadPosRankSum=-0.867;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:57,13:70:99:284,0,1351
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597 chr1 37144 . C T 572.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.027;DP=75;Dels=0.01;FS=19.781;HaplotypeScore=21.1656;MLEAC=1;MLEAF=0.500;MQ=34.13;MQ0=5;MQRankSum=0.880;QD=7.64;ReadPosRankSum=0.119;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:49,25:74:99:601,0,1238
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598 chr1 37145 . G C 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.631;DP=74;Dels=0.00;FS=1.342;HaplotypeScore=17.3626;MLEAC=1;MLEAF=0.500;MQ=33.28;MQ0=5;MQRankSum=-1.467;QD=1.58;ReadPosRankSum=0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),START_GAINED(LOW||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:63,11:74:99:145,0,1687
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599 chr1 37146 . T C 1981.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.057;DP=73;Dels=0.00;FS=1.906;HaplotypeScore=17.3626;MLEAC=2;MLEAF=1.00;MQ=33.50;MQ0=5;MQRankSum=0.070;QD=27.15;ReadPosRankSum=-0.023;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:8,65:73:96:2010,96,0
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600 chr1 37167 . A G 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.120;DP=75;Dels=0.00;FS=11.212;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=30.73;MQ0=5;MQRankSum=-0.123;QD=11.62;ReadPosRankSum=0.029;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:37,38:75:99:900,0,875
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601 chr1 37195 . A C 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.498;DP=63;Dels=0.00;FS=34.326;HaplotypeScore=4.2993;MLEAC=1;MLEAF=0.500;MQ=30.86;MQ0=6;MQRankSum=0.788;QD=4.57;ReadPosRankSum=1.858;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T7|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:47,16:63:99:316,0,1127
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602 chr1 37208 . A C 187.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.181;DP=59;Dels=0.00;FS=17.669;HaplotypeScore=1.7335;MLEAC=1;MLEAF=0.500;MQ=30.82;MQ0=6;MQRankSum=0.988;QD=3.18;ReadPosRankSum=-1.371;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R12|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:47,12:59:99:216,0,1075
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603 chr1 37234 . A G 585.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=21.20;MQ0=5;QD=18.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P20|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,31:31:66:614,66,0
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604 chr1 37263 . G T 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.279;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=28.54;MQ0=4;MQRankSum=-0.748;QD=15.24;ReadPosRankSum=-0.169;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cTc|R30L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:10,26:36:99:577,0,117
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605 chr1 37277 . G A 105.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.511;DP=37;Dels=0.00;FS=1.773;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=34.79;MQ0=3;MQRankSum=-0.596;QD=2.86;ReadPosRankSum=0.085;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D35N|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:27,10:37:99:134,0,662
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606 chr1 37288 . G T 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.241;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=2.7802;MLEAC=1;MLEAF=0.500;MQ=39.98;MQ0=2;MQRankSum=-1.717;QD=2.72;ReadPosRankSum=0.610;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaT|E38D|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:36,11:47:99:156,0,970
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607 chr1 37303 . G A,T 1674.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=2.9926;MLEAC=1,1;MLEAF=0.500,0.500;MQ=46.60;MQ0=1;QD=26.16;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q43H|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q43|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/2:0,54,10:64:99:1936,347,200,1589,0,1559
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608 chr1 37305 . T C 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.346;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=23.7316;MLEAC=1;MLEAF=0.500;MQ=47.52;MQ0=1;MQRankSum=-3.229;QD=1.45;ReadPosRankSum=2.225;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V44A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:58,11:69:99:128,0,1781
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609 chr1 37314 . T C 204.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.448;DP=80;Dels=0.00;FS=1.179;HaplotypeScore=13.7857;MLEAC=1;MLEAF=0.500;MQ=48.12;MQ0=1;MQRankSum=1.805;QD=2.56;ReadPosRankSum=-1.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I47T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:67,13:80:99:233,0,1973
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610 chr1 37336 . T C 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.947;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=2.6540;MLEAC=1;MLEAF=0.500;MQ=48.95;MQ0=0;MQRankSum=2.094;QD=8.05;ReadPosRankSum=0.313;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D54|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:68,31:99:99:825,0,2213
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611 chr1 37361 . C A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.201;DP=104;Dels=0.00;FS=2.268;HaplotypeScore=5.3893;MLEAC=1;MLEAF=0.500;MQ=47.39;MQ0=6;MQRankSum=-1.098;QD=2.63;ReadPosRankSum=1.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P63T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:85,19:104:99:302,0,2484
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612 chr1 37404 . C T 1818.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=39.82;MQ0=7;QD=27.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S77F|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,65:65:99:1847,159,0
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613 chr1 37414 . C A 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.004;DP=53;Dels=0.00;FS=5.282;HaplotypeScore=6.9624;MLEAC=1;MLEAF=0.500;MQ=36.19;MQ0=7;MQRankSum=0.103;QD=3.94;ReadPosRankSum=-1.803;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccA|P80|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:40,13:53:99:237,0,933
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614 chr1 37420 . G A 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.384;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=5.8162;MLEAC=1;MLEAF=0.500;MQ=30.80;MQ0=7;MQRankSum=-0.141;QD=2.92;ReadPosRankSum=-0.424;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A82|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:30,10:40:99:145,0,591
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615 chr1 37458 . C T 161.8 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.06;MQ0=0;QD=12.45;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A95V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,13:13:21:190,21,0
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616 chr1 37459 . A G 199.78 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.74;MQ0=0;QD=14.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A95|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,14:14:24:228,24,0
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617 chr1 37480 . C T 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.442;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=6.5977;MLEAC=1;MLEAF=0.500;MQ=28.74;MQ0=1;MQRankSum=-3.019;QD=0.74;ReadPosRankSum=-1.877;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V102|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:24,11:35:54:54,0,540
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618 chr1 37528 . A T 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.145;DP=99;Dels=0.00;FS=1.426;HaplotypeScore=2.0463;MLEAC=1;MLEAF=0.500;MQ=31.63;MQ0=3;MQRankSum=-2.642;QD=0.76;ReadPosRankSum=1.338;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E118D|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:80,19:99:99:103,0,1690
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619 chr1 37553 . C T 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.618;DP=101;Dels=0.00;FS=0.817;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=32.94;MQ0=5;MQRankSum=-4.815;QD=2.51;ReadPosRankSum=1.481;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L127|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:66,35:101:99:282,0,1683
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620 chr1 37602 . C G 2282.77 . AC=2;AF=1.00;AN=2;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=37.45;MQ0=5;QD=30.04;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S143C|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,76:76:99:2311,186,0
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621 chr1 37607 . T G 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.910;DP=74;Dels=0.00;FS=8.462;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=38.66;MQ0=5;MQRankSum=0.654;QD=9.08;ReadPosRankSum=1.289;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tta/Gta|L145V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:43,31:74:99:700,0,1242
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622 chr1 37632 . T A 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.285;DP=70;Dels=0.00;FS=1.067;HaplotypeScore=165.3085;MLEAC=1;MLEAF=0.500;MQ=39.01;MQ0=2;MQRankSum=-0.738;QD=5.55;ReadPosRankSum=0.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,19:70:99:417,0,1466
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623 chr1 37654 . T C 334.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.313;DP=79;Dels=0.00;FS=1.038;HaplotypeScore=60.4783;MLEAC=1;MLEAF=0.500;MQ=40.53;MQ0=0;MQRankSum=-1.554;QD=4.24;ReadPosRankSum=1.348;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,19:79:99:363,0,1794
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624 chr1 37679 . T C 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=69;Dels=0.01;FS=3.415;HaplotypeScore=131.3512;MLEAC=1;MLEAF=0.500;MQ=36.89;MQ0=2;MQRankSum=0.051;QD=0.20;ReadPosRankSum=-0.256;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,7:68:42:42,0,1556
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625 chr1 37687 . A G 1378.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=69.8232;MLEAC=2;MLEAF=1.00;MQ=34.79;MQ0=2;QD=20.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,65:66:99:1407,129,0
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626 chr1 37807 . C T 3962.77 . AC=2;AF=1.00;AN=2;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.64;MQ0=1;QD=33.77;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,105:105:99:3991,313,0
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627 chr1 37815 . A C 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.480;DP=107;Dels=0.00;FS=2.466;HaplotypeScore=2.4531;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=1;MQRankSum=2.701;QD=2.40;ReadPosRankSum=1.477;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,15:107:99:285,0,3245
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628 chr1 37819 . A G 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.509;DP=106;Dels=0.00;FS=2.428;HaplotypeScore=49.4245;MLEAC=1;MLEAF=0.500;MQ=51.67;MQ0=2;MQRankSum=3.086;QD=2.82;ReadPosRankSum=0.635;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,16:106:99:327,0,3127
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629 chr1 37827 . T C 957.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.964;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=281.8552;MLEAC=1;MLEAF=0.500;MQ=52.18;MQ0=2;MQRankSum=-1.196;QD=9.12;ReadPosRankSum=1.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,36:105:99:986,0,2427
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630 chr1 37829 . G A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.186;DP=103;Dels=0.00;FS=1.099;HaplotypeScore=280.8554;MLEAC=1;MLEAF=0.500;MQ=52.15;MQ0=2;MQRankSum=-5.390;QD=2.67;ReadPosRankSum=-1.865;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,16:103:99:303,0,3052
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631 chr1 37845 . C G 1301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.010;DP=105;Dels=0.00;FS=1.721;HaplotypeScore=34.8876;MLEAC=1;MLEAF=0.500;MQ=54.33;MQ0=2;MQRankSum=-0.287;QD=12.40;ReadPosRankSum=0.867;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,43:105:99:1330,0,2039
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632 chr1 37852 . A T 768.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.963;DP=114;Dels=0.00;FS=7.406;HaplotypeScore=34.8876;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=2;MQRankSum=1.342;QD=6.74;ReadPosRankSum=0.485;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,29:114:99:797,0,2971
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633 chr1 37858 . G T 4069.77 . AC=2;AF=1.00;AN=2;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=23.1962;MLEAC=2;MLEAF=1.00;MQ=55.35;MQ0=2;QD=28.48;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,106:106:99:4098,313,0
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634 chr1 37891 . A G 355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.450;DP=105;Dels=0.00;FS=3.911;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=1;MQRankSum=1.160;QD=3.39;ReadPosRankSum=-1.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,17:105:99:384,0,3122
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635 chr1 37931 . T C 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.853;DP=94;Dels=0.00;FS=6.552;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=3.443;QD=5.77;ReadPosRankSum=-0.138;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,22:94:99:571,0,2560
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636 chr1 37938 . T G 3392.77 . AC=2;AF=1.00;AN=2;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.28;MQ0=0;QD=30.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,88:88:99:3421,259,0
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637 chr1 37969 . A G 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.057;DP=52;Dels=0.00;FS=4.310;HaplotypeScore=2.3113;MLEAC=1;MLEAF=0.500;MQ=57.18;MQ0=0;MQRankSum=-4.200;QD=11.26;ReadPosRankSum=1.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,19:52:99:614,0,1176
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638 chr1 37972 . A G 2052.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=3.3111;MLEAC=2;MLEAF=1.00;MQ=57.23;MQ0=0;QD=26.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,52:53:99:2081,154,0
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639 chr1 37991 . G C 2025.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.39;MQ0=0;QD=27.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2054,153,0
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640 chr1 37996 . T C 1956.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.53;MQ0=0;QD=28.77;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1985,147,0
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641 chr1 37999 . A T 1924.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=57.53;MQ0=0;QD=43.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1953,144,0
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642 chr1 38000 . T C 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.164;DP=50;Dels=0.00;FS=9.868;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.58;MQ0=0;MQRankSum=-4.276;QD=8.80;ReadPosRankSum=-0.402;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:468,0,1240
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643 chr1 38009 . A C 807.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.036;DP=62;Dels=0.00;FS=21.281;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-2.304;QD=13.03;ReadPosRankSum=-3.245;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,26:62:99:836,0,1230
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644 chr1 38043 . C T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.277;DP=66;Dels=0.00;FS=22.795;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.05;MQ0=0;MQRankSum=1.867;QD=15.45;ReadPosRankSum=-2.508;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,32:66:99:1048,0,1191
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645 chr1 38145 . C A 410.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.426;DP=22;Dels=0.00;FS=4.506;HaplotypeScore=20.3295;MLEAC=1;MLEAF=0.500;MQ=56.46;MQ0=0;MQRankSum=1.195;QD=18.67;ReadPosRankSum=-0.253;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:9,13:22:99:439,0,169
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646 chr1 38190 . A C 338.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.579;DP=20;Dels=0.00;FS=37.992;HaplotypeScore=15.6751;MLEAC=1;MLEAF=0.500;MQ=57.69;MQ0=0;MQRankSum=-3.279;QD=16.94;ReadPosRankSum=0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:8,12:20:99:367,0,253
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647 chr1 38209 . G T 1079.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=11.5981;MLEAC=2;MLEAF=1.00;MQ=56.02;MQ0=0;QD=30.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1108,84,0
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648 chr1 38232 . G A 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.397;DP=26;Dels=0.00;FS=45.405;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=0;MQRankSum=-4.243;QD=19.84;ReadPosRankSum=-2.451;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:10,16:26:99:544,0,277
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649 chr1 38259 . T A 394.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.43;MQ0=0;QD=32.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:12:33:423,33,0
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650 chr1 38267 . C T 397.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.95;MQ0=0;QD=23.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:426,33,0
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651 chr1 38269 . G C 393.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.95;MQ0=0;QD=28.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:422,33,0
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652 chr1 38272 . G A 407.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.95;MQ0=0;QD=24.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:436,33,0
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653 chr1 38282 . G A 562.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.42;MQ0=0;QD=27.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:591,45,0
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654 chr1 38290 . T G 1662.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.33;MQ0=0;QD=30.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1691,132,0
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655 chr1 38305 . A G 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.174;DP=54;Dels=0.00;FS=1.164;HaplotypeScore=26.0834;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=0;MQRankSum=-0.232;QD=7.13;ReadPosRankSum=-0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,15:54:99:413,0,1363
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656 chr1 38320 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.621;DP=61;Dels=0.00;FS=5.712;HaplotypeScore=186.2137;MLEAC=1;MLEAF=0.500;MQ=52.26;MQ0=0;MQRankSum=2.727;QD=8.73;ReadPosRankSum=0.530;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,20:61:99:561,0,1414
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657 chr1 38327 . A G 2319.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=146.9227;MLEAC=2;MLEAF=1.00;MQ=53.56;MQ0=0;QD=29.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,61:63:99:2348,184,0
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658 chr1 38332 . G C 474.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.367;DP=64;Dels=0.00;FS=1.052;HaplotypeScore=20.8715;MLEAC=1;MLEAF=0.500;MQ=53.66;MQ0=0;MQRankSum=3.453;QD=7.42;ReadPosRankSum=-2.851;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,19:64:99:503,0,1580
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659 chr1 38333 . G A 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.193;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=20.8715;MLEAC=1;MLEAF=0.500;MQ=53.77;MQ0=0;MQRankSum=-3.324;QD=11.43;ReadPosRankSum=2.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,25:65:99:771,0,1350
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660 chr1 38335 . C T 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.608;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=19.8719;MLEAC=1;MLEAF=0.500;MQ=53.87;MQ0=0;MQRankSum=-3.117;QD=12.89;ReadPosRankSum=1.435;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,27:66:99:879,0,1194
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661 chr1 38344 . C T 2874.77 . AC=2;AF=1.00;AN=2;DP=73;Dels=0.00;FS=0.000;HaplotypeScore=36.8803;MLEAC=2;MLEAF=1.00;MQ=54.82;MQ0=0;QD=32.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,73:73:99:2903,220,0
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662 chr1 38350 . G A 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=33.7387;MLEAC=1;MLEAF=0.500;MQ=55.02;MQ0=0;MQRankSum=2.904;QD=7.78;ReadPosRankSum=-0.189;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:65,26:91:99:736,0,2251
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663 chr1 38352 . G A 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.858;DP=91;Dels=0.00;FS=0.951;HaplotypeScore=33.7387;MLEAC=1;MLEAF=0.500;MQ=55.02;MQ0=0;MQRankSum=3.445;QD=5.45;ReadPosRankSum=0.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,20:91:99:524,0,2399
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664 chr1 38354 . A G 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.325;DP=92;Dels=0.00;FS=1.151;HaplotypeScore=33.7387;MLEAC=1;MLEAF=0.500;MQ=55.08;MQ0=0;MQRankSum=0.796;QD=1.80;ReadPosRankSum=-3.990;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:79,13:92:99:194,0,2761
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665 chr1 38356 . C T 3570.77 . AC=2;AF=1.00;AN=2;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=33.7339;MLEAC=2;MLEAF=1.00;MQ=55.21;MQ0=0;QD=30.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,92:92:99:3599,268,0
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666 chr1 38380 . G C 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=103;Dels=0.00;FS=1.016;HaplotypeScore=5.5532;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=0.452;QD=3.40;ReadPosRankSum=1.646;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,18:103:99:378,0,2986
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667 chr1 38386 . A G 408.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.945;DP=101;Dels=0.00;FS=2.163;HaplotypeScore=5.8191;MLEAC=1;MLEAF=0.500;MQ=58.46;MQ0=0;MQRankSum=1.265;QD=4.05;ReadPosRankSum=2.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:83,18:101:99:437,0,2897
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668 chr1 38406 . A G 581.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.994;DP=110;Dels=0.00;FS=0.886;HaplotypeScore=38.9762;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=2.927;QD=5.29;ReadPosRankSum=1.393;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,24:110:99:610,0,2961
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669 chr1 38410 . G C 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.160;DP=107;Dels=0.00;FS=5.387;HaplotypeScore=39.9755;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=1.092;QD=8.61;ReadPosRankSum=-0.534;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,32:107:99:949,0,2628
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670 chr1 38412 . A G 640.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.025;DP=107;Dels=0.00;FS=1.876;HaplotypeScore=39.9755;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.410;QD=5.99;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,26:107:99:669,0,2864
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671 chr1 38514 . A G 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.579;DP=93;Dels=0.00;FS=5.348;HaplotypeScore=43.8521;MLEAC=1;MLEAF=0.500;MQ=49.76;MQ0=0;MQRankSum=-1.505;QD=3.79;ReadPosRankSum=1.100;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I168V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:73,19:93:99:381,0,2418
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672 chr1 38516 . T G 3066.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.284;DP=85;Dels=0.00;FS=3.166;HaplotypeScore=43.8875;MLEAC=2;MLEAF=1.00;MQ=49.63;MQ0=0;MQRankSum=-0.509;QD=31.58;ReadPosRankSum=1.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atT/atG|I168M|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:1,84:85:99:3095,218,0
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673 chr1 38519 . A C 1258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.706;DP=83;Dels=0.00;FS=18.028;HaplotypeScore=44.8742;MLEAC=1;MLEAF=0.500;MQ=49.02;MQ0=0;MQRankSum=-2.301;QD=15.17;ReadPosRankSum=1.618;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A169|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:40,43:83:99:1287,0,1261
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674 chr1 38524 . G T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.881;DP=87;Dels=0.00;FS=8.398;HaplotypeScore=47.8556;MLEAC=1;MLEAF=0.500;MQ=48.63;MQ0=0;MQRankSum=0.082;QD=6.37;ReadPosRankSum=1.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G171V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:64,23:87:99:582,0,2000
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675 chr1 38580 . G A 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.789;DP=83;Dels=0.00;FS=10.079;HaplotypeScore=4.2557;MLEAC=1;MLEAF=0.500;MQ=42.00;MQ0=0;MQRankSum=1.229;QD=9.35;ReadPosRankSum=-1.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A190T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:49,33:83:99:804,0,1512
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676 chr1 38614 . G T 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.078;DP=88;Dels=0.00;FS=8.617;HaplotypeScore=41.5773;MLEAC=1;MLEAF=0.500;MQ=46.09;MQ0=0;MQRankSum=-1.852;QD=7.99;ReadPosRankSum=-1.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cTc|R201L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:62,26:88:99:731,0,1964
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677 chr1 38616 . C T 1299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.710;DP=88;Dels=0.00;FS=3.034;HaplotypeScore=74.9440;MLEAC=1;MLEAF=0.500;MQ=46.09;MQ0=0;MQRankSum=2.195;QD=14.77;ReadPosRankSum=0.534;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L202|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:45,43:88:99:1328,0,1423
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678 chr1 38621 . C T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.374;DP=92;Dels=0.00;FS=8.548;HaplotypeScore=74.6108;MLEAC=1;MLEAF=0.500;MQ=45.88;MQ0=0;MQRankSum=-2.005;QD=6.60;ReadPosRankSum=-1.676;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N203|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:68,24:92:99:635,0,2194
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679 chr1 38624 . T C 415.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.167;DP=92;Dels=0.00;FS=18.358;HaplotypeScore=71.5984;MLEAC=1;MLEAF=0.500;MQ=45.57;MQ0=0;MQRankSum=-0.682;QD=4.52;ReadPosRankSum=0.966;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A204|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:70,22:92:99:444,0,2305
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680 chr1 38633 . G A 1358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.729;DP=93;Dels=0.00;FS=4.284;HaplotypeScore=20.6300;MLEAC=1;MLEAF=0.500;MQ=46.35;MQ0=0;MQRankSum=1.841;QD=14.61;ReadPosRankSum=0.784;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P207|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:42,51:93:99:1387,0,1217
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681 chr1 38643 . A G 1710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.552;DP=96;Dels=0.00;FS=1.832;HaplotypeScore=4.1979;MLEAC=1;MLEAF=0.500;MQ=45.75;MQ0=0;MQRankSum=1.806;QD=17.82;ReadPosRankSum=1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T211A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:42,54:96:99:1739,0,1020
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682 chr1 38657 . C T 2213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.378;DP=85;Dels=0.00;FS=2.540;HaplotypeScore=14.1583;MLEAC=1;MLEAF=0.500;MQ=45.85;MQ0=1;MQRankSum=1.974;QD=26.04;ReadPosRankSum=1.050;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H215|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:15,70:85:99:2242,0,177
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683 chr1 38659 . A C 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.241;DP=83;Dels=0.00;FS=9.582;HaplotypeScore=13.1589;MLEAC=1;MLEAF=0.500;MQ=45.81;MQ0=1;MQRankSum=1.020;QD=5.08;ReadPosRankSum=-0.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E216A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:63,20:83:99:450,0,1930
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684 chr1 38708 . T C 1093.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.976;DP=42;Dels=0.00;FS=2.564;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.86;MQ0=2;MQRankSum=1.592;QD=26.04;ReadPosRankSum=0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D232|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:3,39:42:29:1122,29,0
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685 chr1 38723 . C T 504.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=4.5678;MLEAC=1;MLEAF=0.500;MQ=34.19;MQ0=2;MQRankSum=1.958;QD=16.83;ReadPosRankSum=-0.432;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S237|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:8,22:30:76:533,0,76
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686 chr1 38732 . C T 190.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.472;DP=25;Dels=0.00;FS=2.077;HaplotypeScore=8.5290;MLEAC=1;MLEAF=0.500;MQ=28.41;MQ0=2;MQRankSum=1.921;QD=7.63;ReadPosRankSum=-1.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F240|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:16,9:25:99:219,0,204
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687 chr1 38739 . A G 239.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.986;DP=21;Dels=0.00;FS=14.564;HaplotypeScore=7.2577;MLEAC=1;MLEAF=0.500;MQ=26.73;MQ0=2;MQRankSum=1.056;QD=11.42;ReadPosRankSum=-1.648;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T243A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:7,14:21:61:268,0,61
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688 chr1 38754 . C T 162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;DP=27;Dels=0.00;FS=23.314;HaplotypeScore=3.4383;MLEAC=1;MLEAF=0.500;MQ=24.11;MQ0=1;MQRankSum=1.291;QD=6.03;ReadPosRankSum=-0.501;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L248|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:17,10:27:99:191,0,164
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689 chr1 38813 . G A 154.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.708;DP=45;Dels=0.00;FS=10.745;HaplotypeScore=6.7165;MLEAC=1;MLEAF=0.500;MQ=23.36;MQ0=6;MQRankSum=0.418;QD=3.44;ReadPosRankSum=-0.933;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T267|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:30,14:45:99:183,0,334
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690 chr1 38818 . G A 239.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.899;DP=44;Dels=0.00;FS=36.491;HaplotypeScore=10.4483;MLEAC=1;MLEAF=0.500;MQ=23.61;MQ0=6;MQRankSum=2.543;QD=5.45;ReadPosRankSum=-1.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C269Y|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:32,12:44:99:268,0,339
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691 chr1 38827 . G T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.662;DP=48;Dels=0.00;FS=16.528;HaplotypeScore=14.4027;MLEAC=1;MLEAF=0.500;MQ=23.16;MQ0=7;MQRankSum=0.544;QD=3.04;ReadPosRankSum=1.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cTc|R272L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:34,14:48:99:174,0,437
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692 chr1 38828 . C T 507.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.199;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=14.4027;MLEAC=1;MLEAF=0.500;MQ=23.63;MQ0=7;MQRankSum=1.593;QD=10.36;ReadPosRankSum=0.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R272|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:16,33:49:99:536,0,103
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693 chr1 38834 . G A 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.131;DP=50;Dels=0.00;FS=1.394;HaplotypeScore=10.1537;MLEAC=1;MLEAF=0.500;MQ=24.71;MQ0=8;MQRankSum=0.472;QD=5.02;ReadPosRankSum=0.341;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R274|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:32,18:50:99:279,0,381
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694 chr1 38874 . G A 270.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.215;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=9.5155;MLEAC=1;MLEAF=0.500;MQ=24.48;MQ0=8;MQRankSum=-0.446;QD=6.30;ReadPosRankSum=0.875;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V288M|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:22,21:43:99:299,0,317
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695 chr1 38881 . G A 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.023;DP=41;Dels=0.00;FS=18.266;HaplotypeScore=21.0278;MLEAC=1;MLEAF=0.500;MQ=26.69;MQ0=6;MQRankSum=0.334;QD=1.80;ReadPosRankSum=-1.159;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C290Y|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:30,11:41:99:102,0,593
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696 chr1 38886 . G A 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.927;DP=42;Dels=0.00;FS=1.336;HaplotypeScore=14.7997;MLEAC=1;MLEAF=0.500;MQ=27.24;MQ0=6;MQRankSum=0.652;QD=4.83;ReadPosRankSum=2.026;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V292I|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:31,11:42:99:231,0,490
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697 chr1 38927 . G A 299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.113;DP=30;Dels=0.00;FS=1.455;HaplotypeScore=5.5545;MLEAC=1;MLEAF=0.500;MQ=33.39;MQ0=1;MQRankSum=-0.895;QD=9.99;ReadPosRankSum=0.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G305|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:15,15:30:99:328,0,330
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698 chr1 38933 . C T 37.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.620;DP=28;Dels=0.00;FS=4.494;HaplotypeScore=6.2885;MLEAC=1;MLEAF=0.500;MQ=33.72;MQ0=0;MQRankSum=-1.020;QD=1.35;ReadPosRankSum=2.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y307|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:23,5:28:66:66,0,561
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699 chr1 38942 . G C 697.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=10.5944;MLEAC=2;MLEAF=1.00;MQ=34.49;MQ0=0;QD=26.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G310|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,26:26:63:726,63,0
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700 chr1 38949 . T C 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.480;DP=23;Dels=0.00;FS=6.415;HaplotypeScore=5.1982;MLEAC=1;MLEAF=0.500;MQ=34.90;MQ0=0;MQRankSum=1.291;QD=14.51;ReadPosRankSum=2.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F313L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:9,14:23:99:362,0,165
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701 chr1 38951 . T G 24.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.960;DP=21;Dels=0.00;FS=2.884;HaplotypeScore=5.1982;MLEAC=1;MLEAF=0.500;MQ=36.04;MQ0=0;MQRankSum=0.151;QD=1.18;ReadPosRankSum=-2.764;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F313L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:18,3:21:53:53,0,465
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702 chr1 38954 . A G 534.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=1.4679;MLEAC=2;MLEAF=1.00;MQ=36.30;MQ0=0;QD=28.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P314|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,19:19:48:563,48,0
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703 chr1 38996 . T G 345.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.00;MQ=32.02;MQ0=1;QD=19.21;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctG|L328|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,13:18:30:374,30,0
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704 chr1 38998 . G A 328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.616;DP=22;Dels=0.00;FS=3.358;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=30.79;MQ0=1;MQRankSum=2.426;QD=14.94;ReadPosRankSum=2.499;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G329E|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:9,13:22:30:357,0,30
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705 chr1 39012 . C T 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.081;DP=31;Dels=0.00;FS=6.864;HaplotypeScore=3.8698;MLEAC=1;MLEAF=0.500;MQ=29.64;MQ0=2;MQRankSum=0.242;QD=0.99;ReadPosRankSum=1.534;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L334|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:25,6:31:59:59,0,466
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706 chr1 39047 . T C 97.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.226;DP=43;Dels=0.00;FS=8.463;HaplotypeScore=12.3919;MLEAC=1;MLEAF=0.500;MQ=26.75;MQ0=5;MQRankSum=0.113;QD=2.27;ReadPosRankSum=-0.038;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D345|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:36,7:43:99:126,0,608
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|
707 chr1 39056 . A T 347.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.448;DP=51;Dels=0.00;FS=13.801;HaplotypeScore=11.9705;MLEAC=1;MLEAF=0.500;MQ=26.54;MQ0=6;MQRankSum=1.911;QD=6.82;ReadPosRankSum=-0.405;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K348N|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:32,19:51:99:376,0,461
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708 chr1 39103 . C T 1400.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=3.9611;MLEAC=2;MLEAF=1.00;MQ=29.47;MQ0=10;QD=21.22;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A364V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,66:66:99:1429,129,0
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709 chr1 39113 . C T 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.057;DP=67;Dels=0.00;FS=2.370;HaplotypeScore=12.4314;MLEAC=1;MLEAF=0.500;MQ=30.14;MQ0=9;MQRankSum=-3.266;QD=8.16;ReadPosRankSum=1.680;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T367|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:26,41:67:99:575,0,677
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|
710 chr1 39116 . T C 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.016;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=10.4367;MLEAC=1;MLEAF=0.500;MQ=29.93;MQ0=9;MQRankSum=3.100;QD=8.41;ReadPosRankSum=-0.858;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y368|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:43,24:67:99:592,0,634
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711 chr1 39117 . G C 1093.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.149;DP=67;Dels=0.00;FS=1.309;HaplotypeScore=10.4367;MLEAC=1;MLEAF=0.500;MQ=29.61;MQ0=9;MQRankSum=1.678;QD=16.32;ReadPosRankSum=-0.336;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ctc|V369L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:18,49:67:99:1122,0,102
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712 chr1 39150 . G A 378.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.147;DP=74;Dels=0.00;FS=5.772;HaplotypeScore=13.8080;MLEAC=1;MLEAF=0.500;MQ=28.74;MQ0=6;MQRankSum=2.238;QD=5.12;ReadPosRankSum=1.855;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E380K|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:57,17:74:99:407,0,823
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713 chr1 39172 . G A 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.714;DP=58;Dels=0.00;FS=4.464;HaplotypeScore=6.4651;MLEAC=1;MLEAF=0.500;MQ=27.39;MQ0=1;MQRankSum=2.790;QD=5.15;ReadPosRankSum=0.121;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R387K|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:44,14:58:99:327,0,622
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714 chr1 39178 . A C 209.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.108;DP=53;Dels=0.00;FS=7.365;HaplotypeScore=8.0329;MLEAC=1;MLEAF=0.500;MQ=27.39;MQ0=0;MQRankSum=2.138;QD=3.96;ReadPosRankSum=0.384;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gCg|E389A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:42,11:53:99:238,0,621
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715 chr1 39240 . C A 821.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.94;MQ0=0;QD=21.07;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P410T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,39:39:78:850,78,0
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|
716 chr1 39253 . G A 804.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.96;MQ0=2;QD=20.64;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R414K|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,39:39:75:833,75,0
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|
717 chr1 39271 . G T 806.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.780;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=5.3949;MLEAC=2;MLEAF=1.00;MQ=26.69;MQ0=8;MQRankSum=2.441;QD=18.34;ReadPosRankSum=1.535;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aTa|R420I|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:9,35:44:50:835,50,0
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|
718 chr1 39276 . G T 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.189;DP=48;Dels=0.00;FS=2.414;HaplotypeScore=5.3949;MLEAC=1;MLEAF=0.500;MQ=27.41;MQ0=9;MQRankSum=0.777;QD=1.14;ReadPosRankSum=-0.609;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ttt|V422F|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:43,5:48:83:83,0,754
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|
719 chr1 39306 . G A 137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.574;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=2.9525;MLEAC=1;MLEAF=0.500;MQ=26.06;MQ0=10;MQRankSum=0.296;QD=2.81;ReadPosRankSum=1.235;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D432N|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:41,8:49:99:166,0,570
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720 chr1 39324 . C T 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.383;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=8.4793;MLEAC=1;MLEAF=0.500;MQ=22.99;MQ0=11;MQRankSum=0.420;QD=3.08;ReadPosRankSum=-0.128;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L438|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:34,12:46:99:170,0,488
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|
721 chr1 39353 . C T 122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.990;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=23.89;MQ0=9;MQRankSum=-0.726;QD=3.15;ReadPosRankSum=-0.286;EFF=SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H447|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:26,13:39:99:151,0,416
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|
722 chr1 39356 . T C 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.526;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=24.07;MQ0=9;MQRankSum=-0.636;QD=1.55;ReadPosRankSum=0.194;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S448|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:27,9:36:84:84,0,463
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|
723 chr1 39366 . C G 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=3.6622;MLEAC=1;MLEAF=0.500;MQ=24.65;MQ0=7;MQRankSum=1.387;QD=13.05;ReadPosRankSum=0.000;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Ggc|R452G|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:8,25:33:68:459,0,68
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724 chr1 39388 . T C 309.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.02;MQ0=2;QD=19.36;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V459A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,16:16:36:338,36,0
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|
725 chr1 39389 . T C 316.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.02;MQ0=2;QD=19.80;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V459|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,16:16:36:345,36,0
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|
|
726 chr1 39403 . T C 290.98 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.255;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=21.86;MQ0=2;MQRankSum=1.104;QD=17.12;ReadPosRankSum=-0.255;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:3,14:17:13:319,13,0
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|
|
727 chr1 39422 . T C 231.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.16;MQ0=1;QD=19.32;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:12:24:260,24,0
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|
|
728 chr1 39447 . T C 117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.212;DP=26;Dels=0.00;FS=9.558;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=31.03;MQ0=4;MQRankSum=2.899;QD=4.53;ReadPosRankSum=-0.862;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,5:26:99:146,0,489
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|
729 chr1 39484 . T C 611.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=1.8320;MLEAC=2;MLEAF=1.00;MQ=30.77;MQ0=3;QD=26.60;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,23:23:51:640,51,0
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|
730 chr1 39510 . G A 129.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.685;DP=20;Dels=0.00;FS=2.963;HaplotypeScore=7.6395;MLEAC=1;MLEAF=0.500;MQ=30.59;MQ0=3;MQRankSum=2.583;QD=6.49;ReadPosRankSum=-0.053;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:15,5:20:99:158,0,271
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|
|
731 chr1 39526 . A G 86.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.749;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=1.8216;MLEAC=1;MLEAF=0.500;MQ=28.66;MQ0=3;MQRankSum=-1.408;QD=6.20;ReadPosRankSum=1.749;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:6,8:14:99:115,0,155
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|
732 chr1 39567 . G C 371.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=21.10;MQ0=1;QD=15.49;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,24:24:42:400,42,0
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|
|
733 chr1 39584 . T C 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.136;DP=38;Dels=0.03;FS=6.990;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.96;MQ0=1;MQRankSum=0.330;QD=14.99;ReadPosRankSum=0.330;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:7,30:37:74:598,0,74
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|
734 chr1 39587 . T C 42.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.311;DP=40;Dels=0.03;FS=7.160;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.64;MQ0=1;MQRankSum=-0.714;QD=1.07;ReadPosRankSum=-0.165;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,7:39:71:71,0,649
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|
|
735 chr1 39596 . A T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.479;DP=52;Dels=0.00;FS=9.385;HaplotypeScore=3.4616;MLEAC=1;MLEAF=0.500;MQ=33.54;MQ0=1;MQRankSum=-1.360;QD=0.76;ReadPosRankSum=0.065;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,8:52:68:68,0,1009
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|
736 chr1 39631 . G A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.488;DP=77;Dels=0.00;FS=1.669;HaplotypeScore=7.9697;MLEAC=1;MLEAF=0.500;MQ=33.50;MQ0=1;MQRankSum=-0.513;QD=0.63;ReadPosRankSum=1.240;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,9:77:77:77,0,1546
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|
737 chr1 39643 . C A 87.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.579;DP=64;Dels=0.00;FS=1.508;HaplotypeScore=19.0317;MLEAC=1;MLEAF=0.500;MQ=34.92;MQ0=0;MQRankSum=0.541;QD=1.37;ReadPosRankSum=-1.004;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,9:64:99:116,0,1373
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|
738 chr1 39644 . T C 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.657;DP=64;Dels=0.00;FS=1.508;HaplotypeScore=19.0317;MLEAC=1;MLEAF=0.500;MQ=34.92;MQ0=0;MQRankSum=0.599;QD=1.54;ReadPosRankSum=-0.966;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,9:64:99:127,0,1357
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|
|
739 chr1 39648 . G C 1350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.749;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=58.2273;MLEAC=1;MLEAF=0.500;MQ=35.15;MQ0=0;MQRankSum=3.645;QD=21.79;ReadPosRankSum=-1.153;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,48:62:58:1379,0,58
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|
|
740 chr1 39651 . C G 1622.77 . AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=56.2590;MLEAC=2;MLEAF=1.00;MQ=36.14;MQ0=0;QD=27.98;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,58:58:99:1651,138,0
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741 chr1 39652 . G A 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.883;DP=58;Dels=0.00;FS=1.714;HaplotypeScore=66.4027;MLEAC=1;MLEAF=0.500;MQ=36.14;MQ0=0;MQRankSum=-1.217;QD=0.34;ReadPosRankSum=0.263;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,7:58:48:48,0,1327
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|
742 chr1 39656 . G A 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.209;DP=58;Dels=0.00;FS=17.787;HaplotypeScore=76.5466;MLEAC=1;MLEAF=0.500;MQ=36.14;MQ0=0;MQRankSum=-3.172;QD=6.93;ReadPosRankSum=1.492;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,25:58:99:430,0,880
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|
743 chr1 39657 . C T 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.197;DP=57;Dels=0.00;FS=10.567;HaplotypeScore=76.5466;MLEAC=1;MLEAF=0.500;MQ=36.40;MQ0=0;MQRankSum=-2.652;QD=3.77;ReadPosRankSum=1.846;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,18:57:99:243,0,1124
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|
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744 chr1 39659 . C T 63.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.644;DP=56;Dels=0.00;FS=3.377;HaplotypeScore=37.1251;MLEAC=1;MLEAF=0.500;MQ=36.35;MQ0=0;MQRankSum=0.246;QD=1.14;ReadPosRankSum=0.199;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,8:56:92:92,0,1236
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745 chr1 39662 . A G 1224.79 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=54.7091;MLEAC=1;MLEAF=0.500;MQ=36.36;MQ0=0;QD=22.68;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,43:54:99:1385,118,0
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746 chr1 39664 . A C 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=2.270;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=53.7676;MLEAC=1;MLEAF=0.500;MQ=36.29;MQ0=0;MQRankSum=-3.301;QD=0.21;ReadPosRankSum=1.393;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,11:53:39:39,0,1193
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747 chr1 39669 . G A 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.015;DP=50;Dels=0.00;FS=1.659;HaplotypeScore=69.6890;MLEAC=1;MLEAF=0.500;MQ=35.68;MQ0=0;MQRankSum=-0.075;QD=0.30;ReadPosRankSum=1.955;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,6:50:43:43,0,1137
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748 chr1 39670 . C T 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.977;DP=44;Dels=0.00;FS=2.860;HaplotypeScore=65.0263;MLEAC=1;MLEAF=0.500;MQ=33.34;MQ0=0;MQRankSum=1.698;QD=6.43;ReadPosRankSum=0.000;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:311,0,662
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749 chr1 39671 . C A 37.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.355;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=69.6870;MLEAC=1;MLEAF=0.500;MQ=33.34;MQ0=0;MQRankSum=-2.765;QD=0.86;ReadPosRankSum=-0.217;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,11:44:66:66,0,915
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750 chr1 39673 . C A 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.953;DP=42;Dels=0.00;FS=4.360;HaplotypeScore=59.5432;MLEAC=1;MLEAF=0.500;MQ=33.27;MQ0=0;MQRankSum=1.563;QD=9.57;ReadPosRankSum=0.902;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:430,0,510
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751 chr1 39676 . G A 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.645;DP=41;Dels=0.00;FS=5.757;HaplotypeScore=49.3994;MLEAC=1;MLEAF=0.500;MQ=33.35;MQ0=0;MQRankSum=-0.931;QD=13.90;ReadPosRankSum=-0.215;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:12,29:41:99:598,0,311
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752 chr1 39678 . G A 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.265;DP=41;Dels=0.00;FS=6.236;HaplotypeScore=49.3994;MLEAC=1;MLEAF=0.500;MQ=33.35;MQ0=0;MQRankSum=1.091;QD=2.77;ReadPosRankSum=1.923;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,7:41:99:142,0,757
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753 chr1 39681 . C T 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.398;DP=40;Dels=0.00;FS=1.360;HaplotypeScore=29.6132;MLEAC=1;MLEAF=0.500;MQ=33.13;MQ0=0;MQRankSum=1.431;QD=6.37;ReadPosRankSum=-0.635;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,12:40:99:283,0,590
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754 chr1 39685 . T C 820.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=10.9898;MLEAC=2;MLEAF=1.00;MQ=34.61;MQ0=0;QD=24.87;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:75:849,75,0
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755 chr1 39710 . A G 29.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.30;MQ0=0;MQRankSum=-0.736;QD=9.93;ReadPosRankSum=0.736;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:1,2:3:29:58,0,29
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756 chr1 39718 . T C 39.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.27;MQ0=0;QD=19.87;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0
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757 chr1 39719 . A G 39.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.27;MQ0=0;QD=19.87;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0
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758 chr1 39722 . C A 37.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.27;MQ0=0;QD=18.87;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:65,6,0
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759 chr1 39725 . A G 39.74 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.42;MQ0=0;QD=13.25;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,3:3:6:67,6,0
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760 chr1 39728 . T C 39.74 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.26;MQ0=0;QD=9.94;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,4:4:6:67,6,0
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761 chr1 39736 . C T 237.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.78;MQ0=0;QD=19.82;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:12:24:266,24,0
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762 chr1 39751 . C T 183.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.423;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=30.63;MQ0=0;MQRankSum=0.930;QD=14.14;ReadPosRankSum=-0.085;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:3,10:13:40:212,0,40
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763 chr1 39756 . G A 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.085;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=30.63;MQ0=0;MQRankSum=0.761;QD=14.60;ReadPosRankSum=-0.085;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:3,10:13:40:218,0,40
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764 chr1 39758 . A G 241.78 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=30.63;MQ0=0;QD=18.60;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:13:24:270,24,0
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765 chr1 39777 . T A 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=21.2570;MLEAC=1;MLEAF=0.500;MQ=36.27;MQ0=0;MQRankSum=1.668;QD=22.67;ReadPosRankSum=-0.927;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:4,21:25:29:595,0,29
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766 chr1 39810 . T C 2246.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.769;DP=69;Dels=0.00;FS=2.663;HaplotypeScore=6.9006;MLEAC=2;MLEAF=1.00;MQ=41.37;MQ0=0;MQRankSum=1.949;QD=32.56;ReadPosRankSum=0.089;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:2,67:69:99:2275,144,0
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767 chr1 39820 . T G 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.337;DP=75;Dels=0.00;FS=0.967;HaplotypeScore=5.9128;MLEAC=1;MLEAF=0.500;MQ=40.90;MQ0=0;MQRankSum=2.599;QD=10.33;ReadPosRankSum=1.672;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,27:75:99:803,0,1331
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768 chr1 39826 . A C 863.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.234;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=2.9758;MLEAC=1;MLEAF=0.500;MQ=40.59;MQ0=0;MQRankSum=2.470;QD=10.80;ReadPosRankSum=0.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,30:80:99:892,0,1425
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769 chr1 39866 . T A 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-3.071;DP=50;Dels=0.04;FS=1.930;HaplotypeScore=58.2750;MLEAC=1;MLEAF=0.500;MQ=43.17;MQ0=0;MQRankSum=0.945;QD=0.48;ReadPosRankSum=-3.645;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,5:48:52:52,0,1435
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770 chr1 39890 . A T 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.405;DP=34;Dels=0.00;FS=6.017;HaplotypeScore=26.6204;MLEAC=1;MLEAF=0.500;MQ=40.76;MQ0=0;MQRankSum=-2.459;QD=5.43;ReadPosRankSum=1.600;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,9:34:99:213,0,772
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771 chr1 39891 . T A 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;DP=43;Dels=0.00;FS=1.596;HaplotypeScore=26.6204;MLEAC=1;MLEAF=0.500;MQ=40.93;MQ0=1;MQRankSum=-2.575;QD=3.44;ReadPosRankSum=2.330;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,9:43:99:176,0,1067
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772 chr1 39914 . A T 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.536;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=23.4102;MLEAC=1;MLEAF=0.500;MQ=40.57;MQ0=4;MQRankSum=0.588;QD=15.15;ReadPosRankSum=-0.170;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:710,0,508
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773 chr1 39960 . C A,T 1177.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=42.42;MQ0=3;QD=25.05;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:0,22,25:47:99:1385,655,589,730,0,673
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774 chr1 39961 . C T 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.209;DP=47;Dels=0.00;FS=1.512;HaplotypeScore=1.7608;MLEAC=1;MLEAF=0.500;MQ=42.42;MQ0=3;MQRankSum=1.537;QD=14.12;ReadPosRankSum=-0.645;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:692,0,570
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775 chr1 39965 . A G 1518.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=2.4258;MLEAC=2;MLEAF=1.00;MQ=42.93;MQ0=0;QD=32.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,43:47:99:1547,126,0
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776 chr1 39976 . A G 1421.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.63;MQ0=0;QD=33.85;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1450,117,0
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777 chr1 39993 . A G 1637.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=30.2512;MLEAC=2;MLEAF=1.00;MQ=43.23;MQ0=0;QD=34.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1666,135,0
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778 chr1 40003 . A G 424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.926;DP=41;Dels=0.00;FS=2.755;HaplotypeScore=36.9270;MLEAC=1;MLEAF=0.500;MQ=41.65;MQ0=0;MQRankSum=-3.665;QD=10.36;ReadPosRankSum=-2.673;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:453,0,706
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779 chr1 40005 . G A 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.023;DP=42;Dels=0.00;FS=12.410;HaplotypeScore=36.9270;MLEAC=1;MLEAF=0.500;MQ=41.54;MQ0=0;MQRankSum=0.221;QD=5.64;ReadPosRankSum=-2.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,10:42:99:265,0,940
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780 chr1 40007 . T A 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.201;DP=42;Dels=0.00;FS=4.327;HaplotypeScore=36.9270;MLEAC=1;MLEAF=0.500;MQ=41.54;MQ0=0;MQRankSum=3.748;QD=16.04;ReadPosRankSum=2.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:702,0,465
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781 chr1 40020 . C T 139.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.607;DP=42;Dels=0.00;FS=15.124;HaplotypeScore=19.7971;MLEAC=1;MLEAF=0.500;MQ=41.55;MQ0=0;MQRankSum=1.991;QD=3.33;ReadPosRankSum=-2.632;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,7:42:99:168,0,1045
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782 chr1 40026 . A G 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=2.995;DP=44;Dels=0.00;FS=1.981;HaplotypeScore=27.1716;MLEAC=1;MLEAF=0.500;MQ=43.19;MQ0=0;MQRankSum=-1.590;QD=0.59;ReadPosRankSum=-0.407;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,5:44:54:54,0,1169
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783 chr1 40027 . C T 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.961;DP=44;Dels=0.00;FS=4.177;HaplotypeScore=27.1716;MLEAC=1;MLEAF=0.500;MQ=43.37;MQ0=0;MQRankSum=-1.590;QD=0.59;ReadPosRankSum=-0.407;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,5:44:54:54,0,1200
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784 chr1 40029 . T C 977.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.378;DP=38;Dels=0.00;FS=1.939;HaplotypeScore=27.1716;MLEAC=1;MLEAF=0.500;MQ=45.09;MQ0=0;MQRankSum=1.977;QD=25.73;ReadPosRankSum=0.067;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:5,32:38:68:1006,0,68
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785 chr1 40032 . T C 1048.85 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.989;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=12.1898;MLEAC=1;MLEAF=0.500;MQ=45.61;MQ0=0;MQRankSum=4.052;QD=28.35;ReadPosRankSum=-2.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:7,30:37:17:1077,0,17
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786 chr1 40037 . G T 1253.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=12.1898;MLEAC=2;MLEAF=1.00;MQ=45.19;MQ0=0;QD=32.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1282,108,0
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787 chr1 40050 . T C 1369.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.02;MQ0=0;QD=33.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1398,117,0
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788 chr1 40053 . C G 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.107;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=5.5950;MLEAC=1;MLEAF=0.500;MQ=50.92;MQ0=0;MQRankSum=1.442;QD=5.73;ReadPosRankSum=-0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,11:46:99:292,0,1057
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789 chr1 40084 . T A 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.742;DP=48;Dels=0.00;FS=1.129;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=0;MQRankSum=0.136;QD=13.27;ReadPosRankSum=-0.512;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,20:48:99:665,0,943
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790 chr1 40096 . G A 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.208;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=0.374;QD=13.50;ReadPosRankSum=-0.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:676,0,875
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791 chr1 40115 . G A 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.138;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=21.9178;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=-0.379;QD=19.83;ReadPosRankSum=-1.244;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,29:48:99:980,0,633
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792 chr1 40186 . A G 2354.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=55.52;MQ0=0;QD=25.20;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2383,181,0
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|
793 chr1 40187 . T C 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.047;DP=65;Dels=0.00;FS=14.460;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=55.60;MQ0=0;MQRankSum=-3.656;QD=0.92;ReadPosRankSum=-1.833;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,9:65:88:88,0,1926
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794 chr1 40200 . A G 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.971;DP=73;Dels=0.00;FS=0.000;HaplotypeScore=16.7520;MLEAC=1;MLEAF=0.500;MQ=54.56;MQ0=0;MQRankSum=0.152;QD=1.71;ReadPosRankSum=-1.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,10:73:99:153,0,2048
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795 chr1 40205 . T C 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.261;DP=74;Dels=0.00;FS=1.321;HaplotypeScore=20.7504;MLEAC=1;MLEAF=0.500;MQ=54.71;MQ0=0;MQRankSum=-4.008;QD=0.46;ReadPosRankSum=2.111;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,10:74:62:62,0,1934
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796 chr1 40212 . G A 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.995;DP=73;Dels=0.00;FS=1.331;HaplotypeScore=32.7378;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=-0.609;QD=2.30;ReadPosRankSum=1.072;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,11:73:99:196,0,1961
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797 chr1 40216 . C T 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.560;DP=77;Dels=0.00;FS=3.483;HaplotypeScore=23.9149;MLEAC=1;MLEAF=0.500;MQ=53.72;MQ0=0;MQRankSum=2.932;QD=7.82;ReadPosRankSum=-1.909;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,25:77:99:630,0,1637
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798 chr1 40235 . A G 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.661;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=35.5558;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-0.751;QD=9.86;ReadPosRankSum=0.430;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,29:80:99:817,0,1701
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799 chr1 40238 . A G 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.173;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=31.6873;MLEAC=1;MLEAF=0.500;MQ=54.96;MQ0=0;MQRankSum=-3.462;QD=5.38;ReadPosRankSum=-2.038;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,22:83:99:475,0,2185
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800 chr1 40257 . G A 1300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.159;DP=89;Dels=0.00;FS=1.765;HaplotypeScore=39.6559;MLEAC=1;MLEAF=0.500;MQ=54.97;MQ0=0;MQRankSum=-4.194;QD=14.62;ReadPosRankSum=-0.491;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,40:89:99:1329,0,1466
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801 chr1 40262 . T C 1269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.662;DP=90;Dels=0.00;FS=12.546;HaplotypeScore=41.5222;MLEAC=1;MLEAF=0.500;MQ=54.41;MQ0=0;MQRankSum=-1.449;QD=14.11;ReadPosRankSum=-0.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,40:90:99:1298,0,1623
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802 chr1 40276 . G A 889.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.940;DP=99;Dels=0.00;FS=2.892;HaplotypeScore=39.6083;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=0;MQRankSum=4.526;QD=8.99;ReadPosRankSum=-0.483;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,30:99:99:918,0,2233
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803 chr1 40279 . A C,G 2850.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=22.6138;MLEAC=1,1;MLEAF=0.500,0.500;MQ=54.31;MQ0=0;QD=28.50;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:0,73,17:100:99:3203,624,407,2579,0,2528
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804 chr1 40299 . T C 90.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.961;DP=94;Dels=0.00;FS=4.739;HaplotypeScore=9.9774;MLEAC=1;MLEAF=0.500;MQ=54.77;MQ0=0;MQRankSum=1.944;QD=0.97;ReadPosRankSum=1.919;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,10:94:99:119,0,2786
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805 chr1 40300 . A G 1244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.818;DP=96;Dels=0.00;FS=2.677;HaplotypeScore=9.9774;MLEAC=1;MLEAF=0.500;MQ=54.67;MQ0=0;MQRankSum=-4.317;QD=12.97;ReadPosRankSum=1.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,43:96:99:1273,0,1762
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806 chr1 40316 . C T 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155;DP=100;Dels=0.00;FS=6.354;HaplotypeScore=64.5095;MLEAC=1;MLEAF=0.500;MQ=54.47;MQ0=0;MQRankSum=-6.856;QD=4.66;ReadPosRankSum=-0.901;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,23:100:99:494,0,2754
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807 chr1 40317 . G A 448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.745;DP=98;Dels=0.00;FS=6.790;HaplotypeScore=64.5095;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=0.824;QD=4.58;ReadPosRankSum=-0.313;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,20:98:99:477,0,2577
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808 chr1 40321 . T A 3751.77 . AC=2;AF=1.00;AN=2;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=68.1412;MLEAC=2;MLEAF=1.00;MQ=54.48;MQ0=0;QD=32.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,98:98:99:3780,292,0
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809 chr1 40326 . T C 1103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.438;DP=102;Dels=0.00;FS=8.509;HaplotypeScore=104.4492;MLEAC=1;MLEAF=0.500;MQ=54.57;MQ0=0;MQRankSum=5.492;QD=10.82;ReadPosRankSum=1.134;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:65,37:102:99:1132,0,2119
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810 chr1 40331 . C T 611.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.325;DP=93;Dels=0.00;FS=0.000;HaplotypeScore=42.7177;MLEAC=1;MLEAF=0.500;MQ=54.62;MQ0=0;MQRankSum=3.620;QD=6.58;ReadPosRankSum=-0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,23:93:99:640,0,2316
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811 chr1 40336 . C T 1086.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.612;DP=89;Dels=0.00;FS=7.137;HaplotypeScore=40.7185;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=4.995;QD=12.21;ReadPosRankSum=0.722;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,34:89:99:1115,0,1717
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812 chr1 40340 . T C 1638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.593;DP=87;Dels=0.00;FS=8.927;HaplotypeScore=60.7684;MLEAC=1;MLEAF=0.500;MQ=55.14;MQ0=0;MQRankSum=-3.839;QD=18.84;ReadPosRankSum=-0.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,52:87:99:1667,0,1091
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813 chr1 40350 . G A 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.570;DP=100;Dels=0.00;FS=2.227;HaplotypeScore=42.2843;MLEAC=1;MLEAF=0.500;MQ=55.57;MQ0=0;MQRankSum=-3.916;QD=2.79;ReadPosRankSum=-0.327;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,18:100:99:307,0,2907
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814 chr1 40357 . A G 1180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.562;DP=101;Dels=0.00;FS=8.331;HaplotypeScore=60.4654;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-3.892;QD=11.69;ReadPosRankSum=-1.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,40:100:99:1209,0,1863
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815 chr1 40359 . T C 3820.77 . AC=2;AF=1.00;AN=2;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=60.4654;MLEAC=2;MLEAF=1.00;MQ=56.15;MQ0=0;QD=29.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,100:101:99:3849,295,0
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816 chr1 40367 . G A 1455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.630;DP=100;Dels=0.00;FS=2.623;HaplotypeScore=40.4721;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=0;MQRankSum=3.679;QD=14.56;ReadPosRankSum=-0.818;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,45:100:99:1484,0,1789
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817 chr1 40385 . A T 307.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.211;DP=99;Dels=0.00;FS=2.269;HaplotypeScore=13.6606;MLEAC=1;MLEAF=0.500;MQ=57.22;MQ0=0;MQRankSum=-2.742;QD=3.11;ReadPosRankSum=-0.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,17:99:99:336,0,2801
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818 chr1 40386 . T C 3699.77 . AC=2;AF=1.00;AN=2;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=13.6606;MLEAC=2;MLEAF=1.00;MQ=57.21;MQ0=0;QD=26.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,100:100:99:3728,298,0
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819 chr1 40390 . C A 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.131;DP=102;Dels=0.00;FS=10.470;HaplotypeScore=47.4671;MLEAC=1;MLEAF=0.500;MQ=57.40;MQ0=0;MQRankSum=-0.627;QD=2.08;ReadPosRankSum=-1.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,14:102:99:240,0,3128
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820 chr1 40397 . T C 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.517;DP=99;Dels=0.00;FS=2.447;HaplotypeScore=91.1211;MLEAC=1;MLEAF=0.500;MQ=57.63;MQ0=0;MQRankSum=-2.184;QD=2.04;ReadPosRankSum=1.270;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,14:99:99:230,0,3009
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821 chr1 40398 . T G 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.071;DP=98;Dels=0.00;FS=0.959;HaplotypeScore=91.9098;MLEAC=1;MLEAF=0.500;MQ=57.61;MQ0=0;MQRankSum=-0.904;QD=4.41;ReadPosRankSum=1.820;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,20:98:99:460,0,2711
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822 chr1 40401 . C A 315.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.162;DP=96;Dels=0.00;FS=2.289;HaplotypeScore=54.1136;MLEAC=1;MLEAF=0.500;MQ=57.86;MQ0=0;MQRankSum=-1.696;QD=3.29;ReadPosRankSum=-0.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,16:96:99:344,0,2884
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823 chr1 40405 . A T 744.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.881;DP=97;Dels=0.00;FS=4.295;HaplotypeScore=68.8441;MLEAC=1;MLEAF=0.500;MQ=57.58;MQ0=0;MQRankSum=1.976;QD=7.68;ReadPosRankSum=-0.753;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,27:97:99:773,0,2466
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824 chr1 40415 . A G 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.202;DP=95;Dels=0.00;FS=4.129;HaplotypeScore=16.3079;MLEAC=1;MLEAF=0.500;MQ=57.68;MQ0=0;MQRankSum=-0.121;QD=2.67;ReadPosRankSum=1.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,14:95:99:282,0,2906
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825 chr1 40423 . G A 715.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.443;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=14.9944;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=-0.719;QD=7.61;ReadPosRankSum=-0.969;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,27:94:99:744,0,2306
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826 chr1 40444 . C T 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.270;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=25.1958;MLEAC=1;MLEAF=0.500;MQ=55.52;MQ0=0;MQRankSum=1.888;QD=4.66;ReadPosRankSum=-0.214;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,18:91:99:452,0,2590
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827 chr1 40450 . C T 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.504;DP=86;Dels=0.00;FS=10.543;HaplotypeScore=36.1917;MLEAC=1;MLEAF=0.500;MQ=54.45;MQ0=0;MQRankSum=-0.407;QD=1.33;ReadPosRankSum=0.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,10:86:99:143,0,2614
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828 chr1 40451 . C T 144.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.552;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=37.1784;MLEAC=1;MLEAF=0.500;MQ=54.45;MQ0=0;MQRankSum=2.698;QD=1.68;ReadPosRankSum=0.430;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,12:86:99:173,0,2633
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829 chr1 40454 . T C 3335.77 . AC=2;AF=1.00;AN=2;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=37.1746;MLEAC=2;MLEAF=1.00;MQ=54.30;MQ0=0;QD=34.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,87:88:99:3364,259,0
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830 chr1 40455 . C T 769.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.977;DP=89;Dels=0.00;FS=5.908;HaplotypeScore=37.1645;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=0.165;QD=8.65;ReadPosRankSum=0.745;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,27:89:99:798,0,2174
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831 chr1 40458 . G A 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.752;DP=90;Dels=0.00;FS=1.024;HaplotypeScore=37.1645;MLEAC=1;MLEAF=0.500;MQ=54.01;MQ0=0;MQRankSum=1.062;QD=3.88;ReadPosRankSum=0.175;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,17:90:99:377,0,2596
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832 chr1 40468 . C T 3532.77 . AC=2;AF=1.00;AN=2;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=32.9796;MLEAC=2;MLEAF=1.00;MQ=53.36;MQ0=0;QD=29.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,94:94:99:3561,277,0
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833 chr1 40469 . C T 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.779;DP=94;Dels=0.00;FS=5.381;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=53.36;MQ0=0;MQRankSum=-1.186;QD=0.15;ReadPosRankSum=2.161;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,8:94:42:42,0,3030
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834 chr1 40480 . C A 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;DP=106;Dels=0.00;FS=4.744;HaplotypeScore=40.7109;MLEAC=1;MLEAF=0.500;MQ=53.17;MQ0=0;MQRankSum=-0.111;QD=4.04;ReadPosRankSum=0.531;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,21:106:99:456,0,3043
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835 chr1 40490 . T C 2948.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.616;DP=107;Dels=0.00;FS=9.034;HaplotypeScore=71.4806;MLEAC=1;MLEAF=0.500;MQ=52.29;MQ0=0;MQRankSum=1.008;QD=27.56;ReadPosRankSum=2.877;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,85:107:99:2977,0,405
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836 chr1 40495 . C G 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.391;DP=114;Dels=0.00;FS=1.985;HaplotypeScore=71.4457;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-0.918;QD=5.58;ReadPosRankSum=1.176;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,23:114:99:664,0,2502
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837 chr1 40497 . G C 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.024;DP=112;Dels=0.00;FS=0.000;HaplotypeScore=69.4473;MLEAC=1;MLEAF=0.500;MQ=51.94;MQ0=0;MQRankSum=-0.543;QD=2.38;ReadPosRankSum=-0.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,17:112:99:295,0,3323
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838 chr1 40511 . A G 3183.76 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.155;DP=116;Dels=0.00;FS=0.000;HaplotypeScore=39.7486;MLEAC=1;MLEAF=0.500;MQ=52.34;MQ0=0;MQRankSum=0.371;QD=27.45;ReadPosRankSum=0.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,92:116:99:3212,0,569
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839 chr1 40524 . G A 358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.064;DP=123;Dels=0.00;FS=2.035;HaplotypeScore=26.4109;MLEAC=1;MLEAF=0.500;MQ=53.69;MQ0=0;MQRankSum=-2.672;QD=2.92;ReadPosRankSum=-0.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:102,21:123:99:387,0,3524
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840 chr1 40526 . G A 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.432;DP=123;Dels=0.00;FS=2.894;HaplotypeScore=26.2780;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-0.204;QD=5.13;ReadPosRankSum=1.764;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,27:123:99:659,0,3056
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841 chr1 40541 . G T 4628.77 . AC=2;AF=1.00;AN=2;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=1.7333;MLEAC=2;MLEAF=1.00;MQ=54.46;MQ0=0;QD=34.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,120:120:99:4657,346,0
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842 chr1 40559 . T A 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.703;DP=122;Dels=0.00;FS=1.745;HaplotypeScore=75.4361;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=0;MQRankSum=3.818;QD=5.47;ReadPosRankSum=1.838;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,27:122:99:695,0,3342
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843 chr1 40562 . C T 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.117;DP=119;Dels=0.00;FS=6.618;HaplotypeScore=120.3506;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=0;MQRankSum=-3.315;QD=3.02;ReadPosRankSum=-1.752;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,20:119:99:388,0,3464
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844 chr1 40565 . G A 408.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.983;DP=115;Dels=0.00;FS=3.367;HaplotypeScore=128.0268;MLEAC=1;MLEAF=0.500;MQ=55.50;MQ0=0;MQRankSum=-0.666;QD=3.55;ReadPosRankSum=-1.487;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,19:115:99:437,0,3355
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845 chr1 40570 . T A 2544.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.959;DP=122;Dels=0.00;FS=0.000;HaplotypeScore=116.1873;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=-4.456;QD=20.86;ReadPosRankSum=-3.072;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,76:122:99:2573,0,1468
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846 chr1 40572 . A G 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.050;DP=126;Dels=0.00;FS=16.724;HaplotypeScore=113.1887;MLEAC=1;MLEAF=0.500;MQ=55.48;MQ0=0;MQRankSum=-3.211;QD=2.10;ReadPosRankSum=-0.566;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:107,19:126:99:293,0,3847
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847 chr1 40574 . G A 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.747;DP=128;Dels=0.00;FS=3.770;HaplotypeScore=81.5684;MLEAC=1;MLEAF=0.500;MQ=55.49;MQ0=0;MQRankSum=1.064;QD=1.61;ReadPosRankSum=1.108;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:111,16:128:99:234,0,3817
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848 chr1 40587 . A G 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.037;DP=153;Dels=0.00;FS=0.744;HaplotypeScore=3.5220;MLEAC=1;MLEAF=0.500;MQ=55.68;MQ0=1;MQRankSum=2.151;QD=5.55;ReadPosRankSum=0.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:119,34:153:99:877,0,4088
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849 chr1 40598 . A T 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.298;DP=145;Dels=0.00;FS=0.898;HaplotypeScore=3.5220;MLEAC=1;MLEAF=0.500;MQ=55.69;MQ0=1;MQRankSum=-3.872;QD=2.10;ReadPosRankSum=2.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:124,21:145:99:333,0,4371
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850 chr1 40601 . T C 315.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.858;DP=141;Dels=0.00;FS=0.951;HaplotypeScore=2.7882;MLEAC=1;MLEAF=0.500;MQ=55.65;MQ0=1;MQRankSum=-4.326;QD=2.24;ReadPosRankSum=3.042;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:122,19:141:99:344,0,4357
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851 chr1 40604 . A G 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.376;DP=140;Dels=0.00;FS=0.952;HaplotypeScore=3.7881;MLEAC=1;MLEAF=0.500;MQ=55.46;MQ0=1;MQRankSum=-4.123;QD=2.30;ReadPosRankSum=3.050;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:121,19:140:99:350,0,4326
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852 chr1 40607 . A T 336.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.747;DP=138;Dels=0.00;FS=2.058;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=55.40;MQ0=1;MQRankSum=-3.796;QD=2.44;ReadPosRankSum=2.787;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:119,19:138:99:365,0,4122
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853 chr1 40613 . T C 379.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.577;DP=138;Dels=0.00;FS=0.884;HaplotypeScore=34.9737;MLEAC=1;MLEAF=0.500;MQ=54.85;MQ0=1;MQRankSum=-4.247;QD=2.75;ReadPosRankSum=0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:116,22:138:99:408,0,4053
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854 chr1 40618 . A G 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.611;DP=140;Dels=0.00;FS=8.579;HaplotypeScore=37.4958;MLEAC=1;MLEAF=0.500;MQ=54.14;MQ0=1;MQRankSum=1.916;QD=0.23;ReadPosRankSum=3.401;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:128,12:140:60:60,0,4583
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855 chr1 40619 . T G 313.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.123;DP=141;Dels=0.00;FS=6.410;HaplotypeScore=37.4958;MLEAC=1;MLEAF=0.500;MQ=54.05;MQ0=1;MQRankSum=-2.776;QD=2.23;ReadPosRankSum=-0.855;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:120,20:141:99:342,0,4240
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856 chr1 40629 . A T 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.928;DP=134;Dels=0.00;FS=0.868;HaplotypeScore=126.7357;MLEAC=1;MLEAF=0.500;MQ=53.57;MQ0=1;MQRankSum=-4.720;QD=3.33;ReadPosRankSum=-1.529;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:112,22:134:99:474,0,3749
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857 chr1 40630 . C T 276.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.225;DP=133;Dels=0.00;FS=2.109;HaplotypeScore=106.7571;MLEAC=1;MLEAF=0.500;MQ=53.52;MQ0=1;MQRankSum=-3.232;QD=2.08;ReadPosRankSum=-0.454;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:113,19:133:99:305,0,3912
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858 chr1 40631 . C T 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.935;DP=134;Dels=0.00;FS=0.896;HaplotypeScore=109.5452;MLEAC=1;MLEAF=0.500;MQ=53.51;MQ0=1;MQRankSum=-4.705;QD=3.01;ReadPosRankSum=-1.132;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:112,21:134:99:432,0,3926
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859 chr1 40635 . C A 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.206;DP=136;Dels=0.00;FS=10.739;HaplotypeScore=148.7017;MLEAC=1;MLEAF=0.500;MQ=53.34;MQ0=1;MQRankSum=5.098;QD=5.45;ReadPosRankSum=-0.010;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,29:136:99:770,0,3047
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860 chr1 40637 . G T 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.363;DP=138;Dels=0.00;FS=1.925;HaplotypeScore=146.7025;MLEAC=1;MLEAF=0.500;MQ=53.22;MQ0=1;MQRankSum=-4.406;QD=3.06;ReadPosRankSum=-1.134;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:116,22:138:99:450,0,4023
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861 chr1 40643 . G A 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=137;Dels=0.00;FS=0.905;HaplotypeScore=80.3353;MLEAC=1;MLEAF=0.500;MQ=53.30;MQ0=1;MQRankSum=-4.704;QD=2.56;ReadPosRankSum=-0.304;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:117,20:137:99:379,0,4082
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862 chr1 40644 . C T 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.833;DP=136;Dels=0.00;FS=0.917;HaplotypeScore=81.3352;MLEAC=1;MLEAF=0.500;MQ=53.25;MQ0=1;MQRankSum=-4.475;QD=2.54;ReadPosRankSum=-0.344;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:116,20:136:99:373,0,4107
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863 chr1 40647 . G A 621.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.428;DP=143;Dels=0.00;FS=7.049;HaplotypeScore=90.1298;MLEAC=1;MLEAF=0.500;MQ=52.42;MQ0=1;MQRankSum=6.086;QD=4.35;ReadPosRankSum=-0.469;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:115,28:143:99:650,0,3953
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864 chr1 40653 . C T 5160.77 . AC=2;AF=1.00;AN=2;DP=138;Dels=0.00;FS=0.000;HaplotypeScore=104.2700;MLEAC=2;MLEAF=1.00;MQ=52.03;MQ0=1;QD=24.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,138:138:99:5189,397,0
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865 chr1 40656 . C A 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.957;DP=136;Dels=0.00;FS=2.901;HaplotypeScore=65.3188;MLEAC=1;MLEAF=0.500;MQ=51.95;MQ0=1;MQRankSum=3.870;QD=4.26;ReadPosRankSum=2.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:109,27:136:99:607,0,3691
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866 chr1 40663 . C T 1219.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.892;DP=131;Dels=0.00;FS=1.470;HaplotypeScore=51.1808;MLEAC=1;MLEAF=0.500;MQ=50.95;MQ0=2;MQRankSum=0.022;QD=9.31;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,44:131:99:1248,0,2916
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867 chr1 40665 . G A 580.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.989;DP=129;Dels=0.00;FS=4.193;HaplotypeScore=50.1809;MLEAC=1;MLEAF=0.500;MQ=50.92;MQ0=2;MQRankSum=3.905;QD=4.50;ReadPosRankSum=1.658;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:101,28:129:99:609,0,3457
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868 chr1 40667 . C A 4617.77 . AC=2;AF=1.00;AN=2;DP=125;Dels=0.00;FS=0.000;HaplotypeScore=25.5251;MLEAC=2;MLEAF=1.00;MQ=50.53;MQ0=2;QD=27.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,125:125:99:4646,352,0
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869 chr1 40679 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=116;Dels=0.00;FS=3.025;HaplotypeScore=31.7934;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=2;MQRankSum=-6.403;QD=4.21;ReadPosRankSum=0.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,25:116:99:517,0,3113
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870 chr1 40680 . C A 609.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.473;DP=116;Dels=0.00;FS=5.789;HaplotypeScore=31.7934;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=2;MQRankSum=3.479;QD=5.26;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,27:116:99:638,0,3045
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871 chr1 40695 . G A 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=109;Dels=0.00;FS=4.432;HaplotypeScore=15.8769;MLEAC=1;MLEAF=0.500;MQ=48.67;MQ0=1;MQRankSum=4.736;QD=1.38;ReadPosRankSum=0.679;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,12:109:99:179,0,3292
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872 chr1 40702 . G A 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.179;DP=118;Dels=0.00;FS=1.878;HaplotypeScore=12.9449;MLEAC=1;MLEAF=0.500;MQ=49.34;MQ0=1;MQRankSum=3.135;QD=5.11;ReadPosRankSum=-1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,24:118:99:631,0,3094
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873 chr1 40724 . C T 2276.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.371;DP=123;Dels=0.00;FS=0.000;HaplotypeScore=76.4647;MLEAC=1;MLEAF=0.500;MQ=50.73;MQ0=1;MQRankSum=-4.544;QD=18.51;ReadPosRankSum=0.815;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,73:123:99:2305,0,1587
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874 chr1 40726 . A G 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.795;DP=121;Dels=0.00;FS=0.855;HaplotypeScore=78.4642;MLEAC=1;MLEAF=0.500;MQ=50.50;MQ0=1;MQRankSum=3.987;QD=5.24;ReadPosRankSum=-0.827;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,25:121:99:662,0,3213
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875 chr1 40730 . T C 2668.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.318;DP=119;Dels=0.00;FS=0.742;HaplotypeScore=131.5265;MLEAC=1;MLEAF=0.500;MQ=50.60;MQ0=1;MQRankSum=-1.336;QD=22.43;ReadPosRankSum=1.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,83:119:99:2697,0,1090
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876 chr1 40731 . T C 163.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.803;DP=119;Dels=0.00;FS=0.000;HaplotypeScore=129.2953;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=1;MQRankSum=-0.479;QD=1.38;ReadPosRankSum=0.553;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:105,14:119:99:192,0,3588
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877 chr1 40742 . C T 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.066;DP=108;Dels=0.00;FS=0.859;HaplotypeScore=18.6626;MLEAC=1;MLEAF=0.500;MQ=51.05;MQ0=1;MQRankSum=-5.117;QD=4.95;ReadPosRankSum=-1.449;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,26:108:99:563,0,2912
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878 chr1 40757 . C T 1092.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.116;DP=119;Dels=0.00;FS=2.628;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=50.49;MQ0=1;MQRankSum=-5.477;QD=9.18;ReadPosRankSum=-1.588;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,42:119:99:1121,0,2615
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879 chr1 40760 . C T 4275.77 . AC=2;AF=1.00;AN=2;DP=117;Dels=0.00;FS=0.000;HaplotypeScore=23.5723;MLEAC=2;MLEAF=1.00;MQ=50.52;MQ0=1;QD=31.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,117:117:99:4304,331,0
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880 chr1 40769 . C T 3289.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.453;DP=123;Dels=0.00;FS=0.861;HaplotypeScore=41.4575;MLEAC=1;MLEAF=0.500;MQ=50.36;MQ0=1;MQRankSum=-4.495;QD=26.75;ReadPosRankSum=-0.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,99:123:99:3318,0,576
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881 chr1 40773 . G A 870.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.272;DP=126;Dels=0.00;FS=2.716;HaplotypeScore=43.4570;MLEAC=1;MLEAF=0.500;MQ=49.93;MQ0=1;MQRankSum=-2.084;QD=6.91;ReadPosRankSum=2.684;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,32:126:99:899,0,2993
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882 chr1 40788 . A C 1705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.951;DP=118;Dels=0.00;FS=2.394;HaplotypeScore=117.6775;MLEAC=1;MLEAF=0.500;MQ=49.33;MQ0=1;MQRankSum=-6.557;QD=14.46;ReadPosRankSum=2.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,62:118:99:1734,0,1876
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883 chr1 40789 . A G 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.778;DP=123;Dels=0.00;FS=11.420;HaplotypeScore=119.6765;MLEAC=1;MLEAF=0.500;MQ=49.20;MQ0=1;MQRankSum=3.191;QD=5.27;ReadPosRankSum=-0.253;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,25:123:99:677,0,3103
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884 chr1 40791 . A G 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.823;DP=121;Dels=0.00;FS=1.004;HaplotypeScore=70.2853;MLEAC=1;MLEAF=0.500;MQ=49.03;MQ0=1;MQRankSum=-4.589;QD=2.12;ReadPosRankSum=1.368;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,24:121:99:285,0,3412
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885 chr1 40795 . A T 129.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.424;DP=125;Dels=0.00;FS=0.000;HaplotypeScore=72.2808;MLEAC=1;MLEAF=0.500;MQ=48.89;MQ0=1;MQRankSum=-2.514;QD=1.04;ReadPosRankSum=2.201;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:108,17:125:99:158,0,3699
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886 chr1 40803 . C T 2015.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.782;DP=118;Dels=0.00;FS=2.491;HaplotypeScore=47.3955;MLEAC=1;MLEAF=0.500;MQ=47.79;MQ0=1;MQRankSum=-6.205;QD=17.08;ReadPosRankSum=-0.663;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,71:118:99:2044,0,1478
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887 chr1 40809 . C T 2959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.887;DP=111;Dels=0.00;FS=0.920;HaplotypeScore=68.1753;MLEAC=1;MLEAF=0.500;MQ=46.88;MQ0=1;MQRankSum=0.903;QD=26.66;ReadPosRankSum=-0.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,91:111:99:2988,0,335
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888 chr1 40816 . G A 454.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.969;DP=113;Dels=0.00;FS=9.418;HaplotypeScore=31.1266;MLEAC=1;MLEAF=0.500;MQ=45.86;MQ0=1;MQRankSum=-1.806;QD=4.02;ReadPosRankSum=0.667;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,20:113:99:483,0,2777
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889 chr1 40819 . T C 4137.77 . AC=2;AF=1.00;AN=2;DP=115;Dels=0.00;FS=0.000;HaplotypeScore=28.2112;MLEAC=2;MLEAF=1.00;MQ=46.60;MQ0=1;QD=33.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,115:115:99:4166,316,0
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890 chr1 40830 . G C 70.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.821;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=19.6261;MLEAC=1;MLEAF=0.500;MQ=46.71;MQ0=1;MQRankSum=-2.358;QD=0.59;ReadPosRankSum=1.325;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:105,15:120:99:99,0,3552
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891 chr1 40833 . C T 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.298;DP=124;Dels=0.00;FS=3.723;HaplotypeScore=34.4038;MLEAC=1;MLEAF=0.500;MQ=46.84;MQ0=1;MQRankSum=-1.292;QD=2.15;ReadPosRankSum=-0.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:104,20:124:99:295,0,3416
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892 chr1 40839 . T C 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.184;DP=119;Dels=0.00;FS=8.132;HaplotypeScore=32.8812;MLEAC=1;MLEAF=0.500;MQ=47.25;MQ0=1;MQRankSum=-0.467;QD=1.86;ReadPosRankSum=0.697;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:102,17:119:99:249,0,3382
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893 chr1 40841 . T A,C 2.14748372629E9 . AC=1,1;AF=0.500,0.500;AN=2;DP=122;Dels=0.00;FS=0.000;HaplotypeScore=19.0976;MLEAC=1,1;MLEAF=0.500,0.500;MQ=47.51;MQ0=1;QD=27.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:0,17,105:122:99:4117,3653,3614,465,0,164
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894 chr1 40851 . C G 787.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.730;DP=129;Dels=0.00;FS=22.816;HaplotypeScore=16.7771;MLEAC=1;MLEAF=0.500;MQ=48.66;MQ0=1;MQRankSum=2.703;QD=6.11;ReadPosRankSum=-0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,30:129:99:816,0,3155
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895 chr1 40863 . T C 1531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.921;DP=118;Dels=0.00;FS=4.700;HaplotypeScore=22.9854;MLEAC=1;MLEAF=0.500;MQ=49.98;MQ0=0;MQRankSum=-4.335;QD=12.98;ReadPosRankSum=0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,57:118:99:1560,0,2100
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896 chr1 40865 . A G 916.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.140;DP=120;Dels=0.00;FS=2.661;HaplotypeScore=22.9854;MLEAC=1;MLEAF=0.500;MQ=50.52;MQ0=0;MQRankSum=-2.918;QD=7.64;ReadPosRankSum=0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,36:120:99:945,0,2823
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897 chr1 40881 . T C 1883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.649;DP=113;Dels=0.00;FS=6.057;HaplotypeScore=16.0432;MLEAC=1;MLEAF=0.500;MQ=52.96;MQ0=0;MQRankSum=-3.511;QD=16.67;ReadPosRankSum=0.917;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,61:113:99:1912,0,1701
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898 chr1 40884 . C T 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.416;DP=112;Dels=0.00;FS=4.487;HaplotypeScore=16.0432;MLEAC=1;MLEAF=0.500;MQ=53.28;MQ0=0;MQRankSum=0.616;QD=0.92;ReadPosRankSum=1.745;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,12:112:99:131,0,3505
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899 chr1 40890 . T C 4000.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.376;DP=108;Dels=0.00;FS=3.638;HaplotypeScore=17.6640;MLEAC=2;MLEAF=1.00;MQ=53.47;MQ0=0;MQRankSum=-1.570;QD=32.92;ReadPosRankSum=-0.761;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,106:108:99:4029,271,0
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900 chr1 40908 . T C 415.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.496;DP=119;Dels=0.00;FS=0.000;HaplotypeScore=8.8927;MLEAC=1;MLEAF=0.500;MQ=54.73;MQ0=0;MQRankSum=-4.713;QD=3.49;ReadPosRankSum=-0.222;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,22:119:99:444,0,3404
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901 chr1 40913 . A T 4662.77 . AC=2;AF=1.00;AN=2;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=7.8494;MLEAC=2;MLEAF=1.00;MQ=54.87;MQ0=0;QD=32.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,119:120:99:4691,355,0
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902 chr1 40932 . T C 4651.77 . AC=2;AF=1.00;AN=2;DP=122;Dels=0.00;FS=0.000;HaplotypeScore=29.4883;MLEAC=2;MLEAF=1.00;MQ=54.22;MQ0=0;QD=32.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,121:122:99:4680,358,0
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903 chr1 40939 . C T 1562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.723;DP=122;Dels=0.00;FS=5.633;HaplotypeScore=53.6940;MLEAC=1;MLEAF=0.500;MQ=53.55;MQ0=0;MQRankSum=-6.420;QD=12.81;ReadPosRankSum=-1.451;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,53:122:99:1591,0,2373
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904 chr1 40942 . G C 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.051;DP=117;Dels=0.00;FS=3.010;HaplotypeScore=52.6941;MLEAC=1;MLEAF=0.500;MQ=53.19;MQ0=0;MQRankSum=2.832;QD=5.14;ReadPosRankSum=2.886;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,24:117:99:630,0,3142
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905 chr1 40949 . A T 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.841;DP=116;Dels=0.00;FS=1.882;HaplotypeScore=91.2099;MLEAC=1;MLEAF=0.500;MQ=51.71;MQ0=1;MQRankSum=2.660;QD=5.38;ReadPosRankSum=3.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,25:116:99:652,0,3037
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906 chr1 40953 . G T 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.177;DP=114;Dels=0.00;FS=4.536;HaplotypeScore=90.5131;MLEAC=1;MLEAF=0.500;MQ=51.22;MQ0=1;MQRankSum=-6.362;QD=4.05;ReadPosRankSum=-0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,25:114:99:490,0,2704
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907 chr1 40963 . C T 1135.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.072;DP=115;Dels=0.00;FS=2.488;HaplotypeScore=45.8271;MLEAC=1;MLEAF=0.500;MQ=50.61;MQ0=1;MQRankSum=-6.812;QD=9.88;ReadPosRankSum=1.154;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,45:115:99:1164,0,2427
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908 chr1 40965 . A C 309.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.064;DP=111;Dels=0.00;FS=1.995;HaplotypeScore=24.4867;MLEAC=1;MLEAF=0.500;MQ=50.29;MQ0=1;MQRankSum=-5.421;QD=2.79;ReadPosRankSum=1.162;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,22:111:99:338,0,3112
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909 chr1 40977 . A G 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.248;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=7.5174;MLEAC=1;MLEAF=0.500;MQ=47.69;MQ0=1;MQRankSum=3.438;QD=5.38;ReadPosRankSum=0.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,25:106:99:598,0,2425
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910 chr1 40988 . C T 336.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.296;DP=97;Dels=0.00;FS=7.020;HaplotypeScore=26.1924;MLEAC=1;MLEAF=0.500;MQ=46.91;MQ0=1;MQRankSum=1.225;QD=3.47;ReadPosRankSum=-0.080;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:79,18:97:99:365,0,2417
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911 chr1 40989 . T C 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.909;DP=94;Dels=0.00;FS=7.233;HaplotypeScore=25.1927;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=1;MQRankSum=1.405;QD=3.77;ReadPosRankSum=-0.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:76,18:94:99:383,0,2284
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912 chr1 40990 . C T 95.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=25.1927;MLEAC=1;MLEAF=0.500;MQ=46.03;MQ0=1;MQRankSum=-4.177;QD=1.04;ReadPosRankSum=2.701;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,15:92:99:124,0,2472
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913 chr1 40992 . A T 2915.77 . AC=2;AF=1.00;AN=2;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=105.3192;MLEAC=2;MLEAF=1.00;MQ=45.42;MQ0=1;QD=33.13;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,88:88:99:2944,235,0
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914 chr1 41013 . C T 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.016;DP=84;Dels=0.00;FS=15.260;HaplotypeScore=153.8354;MLEAC=1;MLEAF=0.500;MQ=39.77;MQ0=1;MQRankSum=0.325;QD=5.07;ReadPosRankSum=1.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,22:84:99:454,0,1750
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915 chr1 41015 . C T 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.276;DP=85;Dels=0.00;FS=1.324;HaplotypeScore=57.0601;MLEAC=1;MLEAF=0.500;MQ=39.97;MQ0=1;MQRankSum=-2.501;QD=0.41;ReadPosRankSum=0.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,10:85:63:63,0,2037
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916 chr1 41017 . T C 2590.77 . AC=2;AF=1.00;AN=2;DP=87;Dels=0.00;FS=0.000;HaplotypeScore=57.5017;MLEAC=2;MLEAF=1.00;MQ=39.87;MQ0=1;QD=29.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,87:87:99:2619,217,0
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917 chr1 41026 . T C 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.073;DP=97;Dels=0.00;FS=3.387;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=40.65;MQ0=1;MQRankSum=1.677;QD=0.36;ReadPosRankSum=-2.910;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,9:97:63:63,0,2499
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918 chr1 41043 . C T 132.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.557;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=33.8776;MLEAC=1;MLEAF=0.500;MQ=42.40;MQ0=1;MQRankSum=0.065;QD=1.44;ReadPosRankSum=0.698;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,12:92:99:161,0,2256
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919 chr1 41046 . G A 68.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.146;DP=89;Dels=0.00;FS=6.728;HaplotypeScore=67.8534;MLEAC=1;MLEAF=0.500;MQ=42.77;MQ0=1;MQRankSum=-2.122;QD=0.77;ReadPosRankSum=1.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,12:89:97:97,0,2293
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920 chr1 41049 . T C 2779.77 . AC=2;AF=1.00;AN=2;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=92.5392;MLEAC=2;MLEAF=1.00;MQ=43.08;MQ0=1;QD=32.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,85:86:99:2808,226,0
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921 chr1 41054 . G A 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.137;DP=87;Dels=0.00;FS=2.873;HaplotypeScore=97.5277;MLEAC=1;MLEAF=0.500;MQ=43.55;MQ0=0;MQRankSum=-1.875;QD=1.18;ReadPosRankSum=1.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,13:87:99:131,0,2231
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922 chr1 41056 . G T 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.880;DP=86;Dels=0.00;FS=12.658;HaplotypeScore=70.2196;MLEAC=1;MLEAF=0.500;MQ=43.45;MQ0=0;MQRankSum=0.504;QD=8.25;ReadPosRankSum=-0.459;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,31:86:99:738,0,1637
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923 chr1 41059 . A T 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.547;DP=85;Dels=0.00;FS=1.923;HaplotypeScore=62.5392;MLEAC=1;MLEAF=0.500;MQ=43.72;MQ0=0;MQRankSum=-1.385;QD=7.07;ReadPosRankSum=2.150;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,28:85:99:629,0,1583
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924 chr1 41064 . C T 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.388;DP=88;Dels=0.00;FS=1.164;HaplotypeScore=86.8690;MLEAC=1;MLEAF=0.500;MQ=44.00;MQ0=0;MQRankSum=-1.609;QD=1.93;ReadPosRankSum=1.221;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,15:88:99:198,0,2343
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925 chr1 41084 . T C 177.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.533;DP=106;Dels=0.00;FS=1.092;HaplotypeScore=17.4304;MLEAC=1;MLEAF=0.500;MQ=47.41;MQ0=0;MQRankSum=-1.180;QD=1.68;ReadPosRankSum=-2.114;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,14:106:99:206,0,3074
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926 chr1 41100 . C A 886.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.112;DP=116;Dels=0.00;FS=0.765;HaplotypeScore=58.6282;MLEAC=1;MLEAF=0.500;MQ=48.59;MQ0=0;MQRankSum=0.652;QD=7.64;ReadPosRankSum=0.622;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,34:116:99:915,0,2691
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927 chr1 41103 . C T 572.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.020;DP=114;Dels=0.00;FS=7.549;HaplotypeScore=60.6270;MLEAC=1;MLEAF=0.500;MQ=49.00;MQ0=0;MQRankSum=0.692;QD=5.02;ReadPosRankSum=-1.089;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,25:114:99:601,0,2970
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928 chr1 41108 . G A 2256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.762;DP=104;Dels=0.00;FS=1.668;HaplotypeScore=55.9666;MLEAC=1;MLEAF=0.500;MQ=50.77;MQ0=0;MQRankSum=-3.973;QD=21.70;ReadPosRankSum=0.215;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,68:104:99:2285,0,1135
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|
|
929 chr1 41121 . C T 1176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.050;DP=106;Dels=0.00;FS=8.022;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=51.15;MQ0=0;MQRankSum=-4.307;QD=11.10;ReadPosRankSum=1.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,39:106:99:1205,0,2309
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|
|
930 chr1 41142 . C A 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.819;DP=93;Dels=0.00;FS=4.344;HaplotypeScore=109.3818;MLEAC=1;MLEAF=0.500;MQ=50.67;MQ0=0;MQRankSum=-3.272;QD=1.78;ReadPosRankSum=-0.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,12:93:99:194,0,2886
|
|
|
931 chr1 41167 . T A 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.059;DP=80;Dels=0.00;FS=2.024;HaplotypeScore=81.4181;MLEAC=1;MLEAF=0.500;MQ=52.03;MQ0=0;MQRankSum=-5.890;QD=8.08;ReadPosRankSum=2.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,24:80:99:675,0,1872
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|
|
932 chr1 41168 . C T 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.548;DP=85;Dels=0.00;FS=1.308;HaplotypeScore=70.7865;MLEAC=1;MLEAF=0.500;MQ=51.72;MQ0=0;MQRankSum=-3.430;QD=1.28;ReadPosRankSum=1.930;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,10:85:99:137,0,2676
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|
|
933 chr1 41170 . C T 195.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.253;DP=86;Dels=0.00;FS=2.556;HaplotypeScore=38.2377;MLEAC=1;MLEAF=0.500;MQ=51.83;MQ0=0;MQRankSum=-4.581;QD=2.28;ReadPosRankSum=2.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,13:86:99:224,0,2606
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|
|
934 chr1 41179 . T C 621.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.172;DP=85;Dels=0.00;FS=0.000;HaplotypeScore=18.4473;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=-4.595;QD=7.31;ReadPosRankSum=-2.191;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,23:85:99:650,0,2189
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|
|
935 chr1 41195 . C G 435.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.737;DP=99;Dels=0.00;FS=3.526;HaplotypeScore=25.2904;MLEAC=1;MLEAF=0.500;MQ=52.58;MQ0=0;MQRankSum=3.710;QD=4.40;ReadPosRankSum=1.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,19:99:99:464,0,2786
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|
|
936 chr1 41199 . C T 552.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.984;DP=96;Dels=0.00;FS=4.808;HaplotypeScore=40.2922;MLEAC=1;MLEAF=0.500;MQ=52.58;MQ0=0;MQRankSum=2.060;QD=5.76;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,22:96:99:581,0,2606
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|
|
937 chr1 41208 . T C 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.073;DP=95;Dels=0.00;FS=3.709;HaplotypeScore=57.4526;MLEAC=1;MLEAF=0.500;MQ=52.97;MQ0=0;MQRankSum=3.607;QD=4.12;ReadPosRankSum=2.665;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,17:95:99:420,0,2797
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|
|
938 chr1 41212 . A C 474.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.288;DP=95;Dels=0.00;FS=0.946;HaplotypeScore=22.4583;MLEAC=1;MLEAF=0.500;MQ=53.16;MQ0=0;MQRankSum=-3.985;QD=5.00;ReadPosRankSum=-1.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,20:95:99:503,0,2582
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|
|
939 chr1 41218 . T A 460.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.830;DP=96;Dels=0.00;FS=2.139;HaplotypeScore=56.9737;MLEAC=1;MLEAF=0.500;MQ=53.88;MQ0=0;MQRankSum=4.681;QD=4.80;ReadPosRankSum=1.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,19:96:99:489,0,2728
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|
|
940 chr1 41224 . C T 1082.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;DP=92;Dels=0.00;FS=8.582;HaplotypeScore=46.8527;MLEAC=1;MLEAF=0.500;MQ=54.51;MQ0=0;MQRankSum=-6.262;QD=11.77;ReadPosRankSum=0.442;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,36:92:99:1111,0,1880
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|
|
941 chr1 41227 . A C 194.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.877;DP=95;Dels=0.00;FS=1.160;HaplotypeScore=73.8186;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=-3.984;QD=2.05;ReadPosRankSum=1.822;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,14:95:99:223,0,2919
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|
|
942 chr1 41234 . A T 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.452;DP=100;Dels=0.00;FS=2.117;HaplotypeScore=65.6546;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=2.503;QD=4.66;ReadPosRankSum=-0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,20:100:99:494,0,2851
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|
|
943 chr1 41236 . T C 22.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.280;DP=101;Dels=0.00;FS=3.152;HaplotypeScore=35.6864;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-3.963;QD=0.23;ReadPosRankSum=0.495;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,9:101:51:51,0,3322
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|
|
944 chr1 41244 . C G 168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.262;DP=106;Dels=0.00;FS=4.109;HaplotypeScore=48.8041;MLEAC=1;MLEAF=0.500;MQ=54.46;MQ0=0;MQRankSum=-2.340;QD=1.59;ReadPosRankSum=0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,13:106:99:197,0,3333
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|
945 chr1 41248 . T C 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.494;DP=109;Dels=0.00;FS=1.115;HaplotypeScore=41.7628;MLEAC=1;MLEAF=0.500;MQ=54.29;MQ0=0;MQRankSum=-3.636;QD=1.78;ReadPosRankSum=0.974;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,14:109:99:222,0,3400
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|
946 chr1 41253 . T A 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.602;DP=119;Dels=0.00;FS=6.215;HaplotypeScore=39.9312;MLEAC=1;MLEAF=0.500;MQ=53.40;MQ0=1;MQRankSum=0.176;QD=4.21;ReadPosRankSum=1.441;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,22:119:99:529,0,3111
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|
|
947 chr1 41254 . A T 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.018;DP=120;Dels=0.00;FS=15.351;HaplotypeScore=39.9312;MLEAC=1;MLEAF=0.500;MQ=53.38;MQ0=1;MQRankSum=-4.673;QD=0.63;ReadPosRankSum=-0.660;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:107,13:120:99:104,0,3713
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|
|
948 chr1 41267 . T A 1376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.520;DP=124;Dels=0.00;FS=10.609;HaplotypeScore=25.9401;MLEAC=1;MLEAF=0.500;MQ=52.51;MQ0=1;MQRankSum=-7.080;QD=11.10;ReadPosRankSum=0.316;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,47:124:99:1405,0,2587
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|
|
949 chr1 41268 . T C 112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=124;Dels=0.00;FS=4.257;HaplotypeScore=82.8206;MLEAC=1;MLEAF=0.500;MQ=52.51;MQ0=1;MQRankSum=-0.901;QD=0.91;ReadPosRankSum=2.028;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:111,13:124:99:141,0,3898
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|
|
950 chr1 41278 . G A 2734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.082;DP=119;Dels=0.00;FS=0.000;HaplotypeScore=36.6252;MLEAC=1;MLEAF=0.500;MQ=52.12;MQ0=1;MQRankSum=1.173;QD=22.98;ReadPosRankSum=0.188;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,80:119:99:2763,0,670
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|
|
951 chr1 41290 . C T 662.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=114;Dels=0.00;FS=0.000;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=51.25;MQ0=1;MQRankSum=-4.504;QD=5.81;ReadPosRankSum=0.748;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,27:114:99:691,0,2884
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|
|
952 chr1 41305 . C T 1582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.376;DP=107;Dels=0.00;FS=1.558;HaplotypeScore=63.7217;MLEAC=1;MLEAF=0.500;MQ=49.95;MQ0=1;MQRankSum=-7.979;QD=14.79;ReadPosRankSum=1.488;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,55:107:99:1611,0,1766
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|
|
953 chr1 41308 . T C 1593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.625;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=62.7218;MLEAC=1;MLEAF=0.500;MQ=49.72;MQ0=1;MQRankSum=-8.201;QD=14.90;ReadPosRankSum=0.708;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,56:107:99:1622,0,1675
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|
|
954 chr1 41310 . C G 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.320;DP=105;Dels=0.00;FS=0.974;HaplotypeScore=62.7218;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=1;MQRankSum=-2.583;QD=3.70;ReadPosRankSum=1.668;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,21:105:99:417,0,2941
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|
|
955 chr1 41313 . T C 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.319;DP=103;Dels=0.00;FS=0.870;HaplotypeScore=103.1863;MLEAC=1;MLEAF=0.500;MQ=49.22;MQ0=1;MQRankSum=4.857;QD=7.01;ReadPosRankSum=0.426;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,26:103:99:750,0,2499
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|
|
956 chr1 41314 . G A,T 1081.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.513;DP=103;Dels=0.00;FS=0.976;HaplotypeScore=42.1919;MLEAC=1,1;MLEAF=0.500,0.500;MQ=49.10;MQ0=1;MQRankSum=-4.684;QD=10.50;ReadPosRankSum=-0.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:21,25,57:103:99:1879,1019,1719,147,0,769
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|
|
957 chr1 41322 . G A 1422.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.564;DP=107;Dels=0.00;FS=1.576;HaplotypeScore=70.4344;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=1;MQRankSum=1.616;QD=13.30;ReadPosRankSum=0.279;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,49:107:99:1451,0,1855
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|
|
958 chr1 41331 . C T 567.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.737;DP=103;Dels=0.00;FS=4.657;HaplotypeScore=99.4972;MLEAC=1;MLEAF=0.500;MQ=48.40;MQ0=1;MQRankSum=4.235;QD=5.51;ReadPosRankSum=2.095;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,22:103:99:596,0,2616
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|
959 chr1 41334 . A C 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.157;DP=101;Dels=0.00;FS=2.142;HaplotypeScore=117.9442;MLEAC=1;MLEAF=0.500;MQ=48.38;MQ0=1;MQRankSum=-2.696;QD=3.51;ReadPosRankSum=0.274;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,19:101:99:383,0,2677
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|
960 chr1 41335 . C A 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.870;DP=98;Dels=0.00;FS=0.996;HaplotypeScore=118.9429;MLEAC=1;MLEAF=0.500;MQ=48.62;MQ0=1;MQRankSum=-3.055;QD=4.25;ReadPosRankSum=-0.712;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,20:98:99:445,0,2383
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|
|
961 chr1 41337 . G A 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.227;DP=99;Dels=0.00;FS=3.218;HaplotypeScore=122.9204;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=1;MQRankSum=2.970;QD=6.55;ReadPosRankSum=0.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,24:99:99:677,0,2337
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|
962 chr1 41343 . G A 508.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.532;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=74.5936;MLEAC=1;MLEAF=0.500;MQ=48.47;MQ0=1;MQRankSum=-3.683;QD=5.19;ReadPosRankSum=1.208;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,25:98:99:537,0,2493
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|
963 chr1 41365 . G A 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.990;DP=86;Dels=0.00;FS=2.433;HaplotypeScore=14.9634;MLEAC=1;MLEAF=0.500;MQ=47.69;MQ0=0;MQRankSum=1.753;QD=3.47;ReadPosRankSum=1.923;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,15:86:99:327,0,2341
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|
|
964 chr1 41375 . T C 2374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=87;Dels=0.00;FS=1.026;HaplotypeScore=33.9683;MLEAC=1;MLEAF=0.500;MQ=49.17;MQ0=0;MQRankSum=-1.561;QD=27.30;ReadPosRankSum=-1.912;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,71:87:99:2403,0,364
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|
965 chr1 41376 . T G 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.803;DP=87;Dels=0.00;FS=4.036;HaplotypeScore=34.9615;MLEAC=1;MLEAF=0.500;MQ=49.58;MQ0=0;MQRankSum=-0.455;QD=3.19;ReadPosRankSum=-0.612;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,15:87:99:306,0,2524
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|
966 chr1 41377 . T C 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.157;DP=88;Dels=0.00;FS=0.884;HaplotypeScore=39.7608;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=0;MQRankSum=-0.490;QD=7.20;ReadPosRankSum=3.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,25:88:99:662,0,2148
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|
|
967 chr1 41395 . A G 319.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.677;DP=84;Dels=0.00;FS=1.101;HaplotypeScore=112.5646;MLEAC=1;MLEAF=0.500;MQ=48.92;MQ0=0;MQRankSum=2.499;QD=3.81;ReadPosRankSum=0.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,15:84:99:348,0,2361
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|
|
968 chr1 41396 . A T 1616.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.249;DP=79;Dels=0.00;FS=3.137;HaplotypeScore=87.3597;MLEAC=1;MLEAF=0.500;MQ=48.75;MQ0=0;MQRankSum=-0.300;QD=20.47;ReadPosRankSum=2.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,50:79:99:1645,0,823
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|
|
969 chr1 41398 . G A 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.022;DP=81;Dels=0.00;FS=3.484;HaplotypeScore=80.5740;MLEAC=1;MLEAF=0.500;MQ=49.12;MQ0=0;MQRankSum=-1.669;QD=8.63;ReadPosRankSum=1.405;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,24:81:99:727,0,1467
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|
|
970 chr1 41404 . T C 2294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=97;Dels=0.00;FS=0.832;HaplotypeScore=104.9252;MLEAC=1;MLEAF=0.500;MQ=48.15;MQ0=0;MQRankSum=4.062;QD=23.66;ReadPosRankSum=2.116;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,68:97:99:2323,0,710
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971 chr1 41409 . C T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.386;DP=105;Dels=0.00;FS=11.861;HaplotypeScore=51.0534;MLEAC=1;MLEAF=0.500;MQ=48.48;MQ0=0;MQRankSum=-4.669;QD=0.65;ReadPosRankSum=-2.162;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,13:105:96:96,0,3129
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972 chr1 41415 . G A 335.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.786;DP=107;Dels=0.00;FS=11.635;HaplotypeScore=15.7947;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=0;MQRankSum=1.795;QD=3.14;ReadPosRankSum=-0.937;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,18:107:99:364,0,2936
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973 chr1 41433 . A G 1679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.407;DP=111;Dels=0.00;FS=3.563;HaplotypeScore=105.5605;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=0;MQRankSum=-5.707;QD=15.13;ReadPosRankSum=1.023;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,57:111:99:1708,0,1780
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974 chr1 41435 . A G 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.631;DP=109;Dels=0.00;FS=17.321;HaplotypeScore=102.6178;MLEAC=1;MLEAF=0.500;MQ=49.30;MQ0=0;MQRankSum=-4.352;QD=0.94;ReadPosRankSum=2.286;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,13:109:99:131,0,3341
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975 chr1 41438 . T G 3087.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.252;DP=111;Dels=0.00;FS=11.712;HaplotypeScore=118.7379;MLEAC=1;MLEAF=0.500;MQ=49.38;MQ0=0;MQRankSum=0.604;QD=27.82;ReadPosRankSum=0.156;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,93:111:99:3116,0,375
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976 chr1 41441 . C T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;DP=115;Dels=0.00;FS=6.121;HaplotypeScore=118.1844;MLEAC=1;MLEAF=0.500;MQ=49.65;MQ0=0;MQRankSum=5.083;QD=5.02;ReadPosRankSum=-0.127;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,24:115:99:605,0,2982
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977 chr1 41447 . C T 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.963;DP=113;Dels=0.00;FS=2.061;HaplotypeScore=55.8367;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-4.171;QD=3.53;ReadPosRankSum=-0.765;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,22:113:99:427,0,3162
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978 chr1 41451 . T C 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.403;DP=114;Dels=0.00;FS=25.914;HaplotypeScore=63.6216;MLEAC=1;MLEAF=0.500;MQ=50.72;MQ0=0;MQRankSum=-4.658;QD=1.12;ReadPosRankSum=3.544;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,14:114:99:156,0,3508
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979 chr1 41458 . T G 2070.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.880;DP=118;Dels=0.00;FS=0.000;HaplotypeScore=14.9365;MLEAC=1;MLEAF=0.500;MQ=50.88;MQ0=0;MQRankSum=-8.252;QD=17.55;ReadPosRankSum=0.234;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,67:118:99:2099,0,1630
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980 chr1 41472 . G A 631.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.270;DP=118;Dels=0.00;FS=4.281;HaplotypeScore=23.8857;MLEAC=1;MLEAF=0.500;MQ=51.16;MQ0=0;MQRankSum=4.715;QD=5.35;ReadPosRankSum=1.357;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,25:118:99:660,0,3092
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981 chr1 41477 . C T 261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.320;DP=116;Dels=0.00;FS=24.979;HaplotypeScore=26.4514;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-4.819;QD=2.26;ReadPosRankSum=-1.044;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:98,17:116:99:290,0,3370
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982 chr1 41490 . C T 1347.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.253;DP=120;Dels=0.00;FS=7.377;HaplotypeScore=103.2713;MLEAC=1;MLEAF=0.500;MQ=51.74;MQ0=0;MQRankSum=-4.581;QD=11.23;ReadPosRankSum=-1.204;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,43:120:99:1376,0,2560
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983 chr1 41492 . G A 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.358;DP=122;Dels=0.00;FS=4.136;HaplotypeScore=109.9755;MLEAC=1;MLEAF=0.500;MQ=51.38;MQ0=0;MQRankSum=-5.075;QD=4.19;ReadPosRankSum=0.670;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,27:122:99:540,0,3167
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984 chr1 41495 . C T 1275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.359;DP=120;Dels=0.00;FS=6.076;HaplotypeScore=130.0290;MLEAC=1;MLEAF=0.500;MQ=51.38;MQ0=0;MQRankSum=-4.101;QD=10.63;ReadPosRankSum=-0.859;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,42:120:99:1304,0,2562
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985 chr1 41499 . C T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.190;DP=121;Dels=0.00;FS=8.830;HaplotypeScore=131.1958;MLEAC=1;MLEAF=0.500;MQ=51.52;MQ0=0;MQRankSum=4.822;QD=5.84;ReadPosRankSum=0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,27:121:99:735,0,3300
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986 chr1 41500 . C A 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=123;Dels=0.00;FS=4.152;HaplotypeScore=131.1958;MLEAC=1;MLEAF=0.500;MQ=51.46;MQ0=0;MQRankSum=-4.922;QD=4.27;ReadPosRankSum=2.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,26:123:99:554,0,3500
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987 chr1 41503 . T C 2252.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=119;Dels=0.00;FS=4.440;HaplotypeScore=73.1398;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=-7.475;QD=18.93;ReadPosRankSum=0.616;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,69:119:99:2281,0,1652
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988 chr1 41543 . G A 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.119;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=33.5509;MLEAC=1;MLEAF=0.500;MQ=45.79;MQ0=0;MQRankSum=1.422;QD=1.67;ReadPosRankSum=0.051;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,12:94:99:185,0,2657
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989 chr1 41544 . C A 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.603;DP=94;Dels=0.00;FS=5.349;HaplotypeScore=33.5509;MLEAC=1;MLEAF=0.500;MQ=45.79;MQ0=0;MQRankSum=0.591;QD=4.56;ReadPosRankSum=-0.548;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,20:94:99:457,0,2138
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990 chr1 41546 . A G 3381.77 . AC=2;AF=1.00;AN=2;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=27.5019;MLEAC=2;MLEAF=1.00;MQ=45.55;MQ0=0;QD=31.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,94:95:99:3410,268,0
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991 chr1 41562 . G A 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.388;DP=90;Dels=0.00;FS=3.007;HaplotypeScore=34.8266;MLEAC=1;MLEAF=0.500;MQ=42.64;MQ0=0;MQRankSum=-0.632;QD=6.88;ReadPosRankSum=0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,28:90:99:647,0,1945
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992 chr1 41564 . C T 101.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=55.5562;MLEAC=1;MLEAF=0.500;MQ=41.85;MQ0=0;MQRankSum=1.630;QD=1.23;ReadPosRankSum=1.364;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,10:83:99:130,0,2184
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993 chr1 41566 . C A 2583.77 . AC=2;AF=1.00;AN=2;DP=77;Dels=0.00;FS=0.000;HaplotypeScore=62.4145;MLEAC=2;MLEAF=1.00;MQ=41.29;MQ0=0;QD=33.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,77:77:99:2612,211,0
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994 chr1 41569 . T C 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.046;DP=76;Dels=0.00;FS=3.973;HaplotypeScore=65.4132;MLEAC=1;MLEAF=0.500;MQ=40.71;MQ0=0;MQRankSum=1.851;QD=5.79;ReadPosRankSum=0.055;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,18:76:99:468,0,1633
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995 chr1 41572 . T C 2032.9 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.322;DP=75;Dels=0.00;FS=1.682;HaplotypeScore=65.4132;MLEAC=1;MLEAF=0.500;MQ=40.70;MQ0=0;MQRankSum=-0.869;QD=27.11;ReadPosRankSum=-0.537;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:6,69:75:15:2061,0,15
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996 chr1 41574 . G T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.327;DP=76;Dels=0.00;FS=3.699;HaplotypeScore=53.4650;MLEAC=1;MLEAF=0.500;MQ=40.15;MQ0=0;MQRankSum=0.032;QD=9.00;ReadPosRankSum=3.623;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,25:76:99:712,0,1145
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997 chr1 41576 . A T 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.035;DP=83;Dels=0.00;FS=1.310;HaplotypeScore=45.4818;MLEAC=1;MLEAF=0.500;MQ=40.13;MQ0=0;MQRankSum=-1.812;QD=0.39;ReadPosRankSum=-0.301;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,10:83:61:61,0,2187
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998 chr1 41587 . C T 940.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.239;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=59.1819;MLEAC=1;MLEAF=0.500;MQ=39.01;MQ0=0;MQRankSum=2.270;QD=10.01;ReadPosRankSum=1.892;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,34:94:99:969,0,1542
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999 chr1 41588 . T A 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.902;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=56.1832;MLEAC=1;MLEAF=0.500;MQ=38.88;MQ0=0;MQRankSum=-1.330;QD=3.74;ReadPosRankSum=2.028;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,21:92:99:372,0,2076
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1000 chr1 41593 . A G 2833.77 . AC=2;AF=1.00;AN=2;DP=89;Dels=0.00;FS=0.000;HaplotypeScore=51.2291;MLEAC=2;MLEAF=1.00;MQ=39.22;MQ0=0;QD=31.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,89:89:99:2862,241,0
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1001 chr1 41597 . T A 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.834;DP=93;Dels=0.00;FS=1.013;HaplotypeScore=58.9239;MLEAC=1;MLEAF=0.500;MQ=39.40;MQ0=0;MQRankSum=-1.253;QD=3.26;ReadPosRankSum=-0.777;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,19:93:99:331,0,2049
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1002 chr1 41612 . T C 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.547;DP=94;Dels=0.00;FS=3.843;HaplotypeScore=30.0447;MLEAC=1;MLEAF=0.500;MQ=39.90;MQ0=0;MQRankSum=-1.714;QD=1.66;ReadPosRankSum=-0.857;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:79,15:94:99:184,0,2308
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1003 chr1 41623 . C T 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.855;DP=95;Dels=0.00;FS=1.274;HaplotypeScore=34.4885;MLEAC=1;MLEAF=0.500;MQ=41.23;MQ0=0;MQRankSum=-1.146;QD=0.23;ReadPosRankSum=-2.116;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,10:95:50:50,0,2553
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1004 chr1 41633 . C T 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.040;DP=97;Dels=0.00;FS=0.962;HaplotypeScore=42.7026;MLEAC=1;MLEAF=0.500;MQ=41.75;MQ0=0;MQRankSum=-1.768;QD=4.76;ReadPosRankSum=1.633;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,23:97:99:490,0,2247
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1005 chr1 41638 . T G 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.578;DP=99;Dels=0.00;FS=11.653;HaplotypeScore=45.8263;MLEAC=1;MLEAF=0.500;MQ=42.14;MQ0=0;MQRankSum=1.485;QD=4.36;ReadPosRankSum=-0.312;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,21:99:99:460,0,2342
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1006 chr1 41640 . A T 3476.77 . AC=2;AF=1.00;AN=2;DP=102;Dels=0.00;FS=0.000;HaplotypeScore=43.8379;MLEAC=2;MLEAF=1.00;MQ=42.75;MQ0=0;QD=34.09;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,102:102:99:3505,280,0
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1007 chr1 41642 . C T 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.284;DP=102;Dels=0.00;FS=4.287;HaplotypeScore=43.8379;MLEAC=1;MLEAF=0.500;MQ=42.97;MQ0=0;MQRankSum=-1.538;QD=0.99;ReadPosRankSum=0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,12:102:99:129,0,2667
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1008 chr1 41645 . G A 192.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.552;DP=106;Dels=0.00;FS=2.304;HaplotypeScore=28.8553;MLEAC=1;MLEAF=0.500;MQ=42.92;MQ0=0;MQRankSum=-1.566;QD=1.82;ReadPosRankSum=-1.328;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,16:106:99:221,0,2816
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1009 chr1 41657 . T C 458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.271;DP=113;Dels=0.00;FS=4.518;HaplotypeScore=64.9583;MLEAC=1;MLEAF=0.500;MQ=44.13;MQ0=0;MQRankSum=-2.414;QD=4.06;ReadPosRankSum=1.615;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,23:113:99:487,0,2786
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1010 chr1 41663 . A T 154.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.503;DP=114;Dels=0.00;FS=3.858;HaplotypeScore=81.6675;MLEAC=1;MLEAF=0.500;MQ=45.09;MQ0=0;MQRankSum=-1.442;QD=1.36;ReadPosRankSum=1.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,15:114:99:183,0,3367
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1011 chr1 41665 . T A 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.927;DP=113;Dels=0.00;FS=3.826;HaplotypeScore=81.6675;MLEAC=1;MLEAF=0.500;MQ=45.28;MQ0=0;MQRankSum=-1.612;QD=1.48;ReadPosRankSum=1.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:98,15:113:99:196,0,3343
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1012 chr1 41669 . A G 249.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.192;DP=119;Dels=0.00;FS=4.933;HaplotypeScore=68.0952;MLEAC=1;MLEAF=0.500;MQ=45.13;MQ0=0;MQRankSum=-1.839;QD=2.10;ReadPosRankSum=0.185;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,19:119:99:278,0,3198
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1013 chr1 41678 . T C 357.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.051;DP=115;Dels=0.00;FS=6.885;HaplotypeScore=79.4081;MLEAC=1;MLEAF=0.500;MQ=46.17;MQ0=0;MQRankSum=-3.479;QD=3.11;ReadPosRankSum=3.870;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,20:115:99:386,0,3047
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1014 chr1 41679 . G A 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.748;DP=111;Dels=0.00;FS=3.602;HaplotypeScore=78.4123;MLEAC=1;MLEAF=0.500;MQ=46.33;MQ0=0;MQRankSum=-3.517;QD=2.09;ReadPosRankSum=-0.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,17:111:99:260,0,3158
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1015 chr1 41680 . A C 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.471;DP=108;Dels=0.00;FS=1.071;HaplotypeScore=58.7186;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=0;MQRankSum=-3.109;QD=1.71;ReadPosRankSum=0.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,15:108:99:213,0,3172
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1016 chr1 41687 . G C 146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.837;DP=112;Dels=0.00;FS=2.333;HaplotypeScore=58.7186;MLEAC=1;MLEAF=0.500;MQ=45.86;MQ0=0;MQRankSum=-2.828;QD=1.31;ReadPosRankSum=-0.085;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,15:112:99:175,0,3221
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1017 chr1 41717 . G C 191.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.104;DP=101;Dels=0.00;FS=10.379;HaplotypeScore=39.1666;MLEAC=1;MLEAF=0.500;MQ=42.12;MQ0=0;MQRankSum=-0.222;QD=1.90;ReadPosRankSum=2.162;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,15:101:99:220,0,2653
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1018 chr1 41723 . C T 731.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.845;DP=104;Dels=0.00;FS=7.631;HaplotypeScore=57.0647;MLEAC=1;MLEAF=0.500;MQ=41.47;MQ0=0;MQRankSum=0.585;QD=7.04;ReadPosRankSum=0.319;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,30:104:99:760,0,2081
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1019 chr1 41727 . T C 1110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.538;DP=103;Dels=0.00;FS=25.678;HaplotypeScore=89.0081;MLEAC=1;MLEAF=0.500;MQ=41.42;MQ0=0;MQRankSum=-2.718;QD=10.78;ReadPosRankSum=-0.518;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,43:103:99:1139,0,1804
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1020 chr1 41733 . C T 126.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.025;DP=101;Dels=0.00;FS=8.661;HaplotypeScore=68.3374;MLEAC=1;MLEAF=0.500;MQ=40.86;MQ0=0;MQRankSum=0.319;QD=1.26;ReadPosRankSum=0.380;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,13:101:99:155,0,2688
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1021 chr1 41737 . G A 28.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.067;DP=98;Dels=0.00;FS=1.384;HaplotypeScore=41.8358;MLEAC=1;MLEAF=0.500;MQ=41.09;MQ0=0;MQRankSum=-0.972;QD=0.29;ReadPosRankSum=-2.706;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,9:98:57:57,0,2778
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1022 chr1 41760 . C T 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.711;DP=84;Dels=0.00;FS=4.638;HaplotypeScore=16.6682;MLEAC=1;MLEAF=0.500;MQ=38.94;MQ0=0;MQRankSum=2.250;QD=7.74;ReadPosRankSum=1.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,26:84:99:678,0,1606
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1023 chr1 41790 . C T 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.449;DP=72;Dels=0.00;FS=0.904;HaplotypeScore=22.5923;MLEAC=1;MLEAF=0.500;MQ=41.27;MQ0=0;MQRankSum=1.292;QD=12.39;ReadPosRankSum=1.235;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,34:72:99:920,0,1016
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1024 chr1 41797 . T G 248.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.769;DP=56;Dels=0.00;FS=17.110;HaplotypeScore=26.2547;MLEAC=1;MLEAF=0.500;MQ=44.99;MQ0=0;MQRankSum=0.349;QD=4.44;ReadPosRankSum=1.488;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,12:56:99:277,0,1304
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1025 chr1 41816 . T C 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.517;DP=70;Dels=0.00;FS=19.980;HaplotypeScore=12.2986;MLEAC=1;MLEAF=0.500;MQ=44.44;MQ0=0;MQRankSum=1.485;QD=5.95;ReadPosRankSum=0.894;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,18:70:99:445,0,1433
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1026 chr1 41832 . A G 332.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.295;DP=72;Dels=0.00;FS=47.755;HaplotypeScore=25.8822;MLEAC=1;MLEAF=0.500;MQ=46.32;MQ0=1;MQRankSum=-5.914;QD=4.62;ReadPosRankSum=0.334;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,25:72:99:361,0,1584
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1027 chr1 41839 . T C 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.104;DP=75;Dels=0.00;FS=46.700;HaplotypeScore=23.9247;MLEAC=1;MLEAF=0.500;MQ=46.37;MQ0=1;MQRankSum=-6.222;QD=5.20;ReadPosRankSum=0.198;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,27:75:99:418,0,1578
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1028 chr1 41841 . A G 1684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.470;DP=73;Dels=0.00;FS=17.617;HaplotypeScore=23.9247;MLEAC=1;MLEAF=0.500;MQ=46.38;MQ0=1;MQRankSum=3.993;QD=23.08;ReadPosRankSum=2.343;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,57:73:99:1713,0,219
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1029 chr1 41855 . A G 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.819;DP=75;Dels=0.00;FS=34.596;HaplotypeScore=5.5757;MLEAC=1;MLEAF=0.500;MQ=46.37;MQ0=4;MQRankSum=-4.879;QD=2.30;ReadPosRankSum=2.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,17:75:99:201,0,1834
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1030 chr1 41867 . C T 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.675;DP=76;Dels=0.00;FS=7.041;HaplotypeScore=8.7104;MLEAC=1;MLEAF=0.500;MQ=45.61;MQ0=4;MQRankSum=4.354;QD=8.84;ReadPosRankSum=-1.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,24:76:99:700,0,1282
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1031 chr1 41874 . C T 27.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.555;DP=75;Dels=0.00;FS=14.535;HaplotypeScore=9.9168;MLEAC=1;MLEAF=0.500;MQ=45.20;MQ0=4;MQRankSum=-3.082;QD=0.37;ReadPosRankSum=2.228;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,9:75:56:56,0,1930
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1032 chr1 41875 . C T 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.568;DP=73;Dels=0.00;FS=5.210;HaplotypeScore=9.9168;MLEAC=1;MLEAF=0.500;MQ=45.03;MQ0=4;MQRankSum=3.339;QD=10.49;ReadPosRankSum=-1.991;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,25:73:99:794,0,1121
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1033 chr1 41887 . T C 2160.77 . AC=2;AF=1.00;AN=2;DP=70;Dels=0.00;FS=0.000;HaplotypeScore=18.1629;MLEAC=2;MLEAF=1.00;MQ=45.19;MQ0=4;QD=30.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,70:70:99:2189,175,0
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1034 chr1 41891 . A G 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.175;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=76.6927;MLEAC=1;MLEAF=0.500;MQ=45.05;MQ0=4;MQRankSum=1.412;QD=10.65;ReadPosRankSum=0.443;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,24:69:99:763,0,786
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1035 chr1 41899 . T A 1216.94 . AC=2;AF=1.00;AN=2;BaseQRankSum=-2.812;DP=52;Dels=0.02;FS=6.283;HaplotypeScore=36.3869;MLEAC=2;MLEAF=1.00;MQ=46.58;MQ0=4;MQRankSum=3.157;QD=23.40;ReadPosRankSum=-0.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:9,42:51:14:1245,14,0
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1036 chr1 41900 . T C 1523.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.417;DP=52;Dels=0.00;FS=5.909;HaplotypeScore=45.3219;MLEAC=2;MLEAF=1.00;MQ=46.58;MQ0=4;MQRankSum=3.172;QD=29.30;ReadPosRankSum=-0.304;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:9,43:52:29:1552,29,0
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1037 chr1 41931 . C T 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.318;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=48.90;MQ0=3;MQRankSum=0.304;QD=11.97;ReadPosRankSum=1.648;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,31:65:99:806,0,1148
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1038 chr1 41944 . C G 2024.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9734;MLEAC=2;MLEAF=1.00;MQ=51.55;MQ0=0;QD=32.52;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2053,156,0
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1039 chr1 41946 . T C 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.696;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=51.55;MQ0=0;MQRankSum=-0.278;QD=14.11;ReadPosRankSum=1.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:776,0,935
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1040 chr1 41952 . T C 1861.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.38;MQ0=0;QD=36.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1890,144,0
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1041 chr1 41954 . G A 783.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.165;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.11;MQ0=0;MQRankSum=-0.942;QD=15.68;ReadPosRankSum=0.515;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:812,0,822
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1042 chr1 41991 . C T 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.008;DP=56;Dels=0.00;FS=7.656;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=50.73;MQ0=0;MQRankSum=1.035;QD=12.37;ReadPosRankSum=0.654;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:721,0,1091
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1043 chr1 42007 . G A 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.444;DP=51;Dels=0.00;FS=10.314;HaplotypeScore=2.4441;MLEAC=1;MLEAF=0.500;MQ=50.10;MQ0=0;MQRankSum=1.161;QD=13.51;ReadPosRankSum=-1.613;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:717,0,897
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1044 chr1 42036 . A G 1816.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=4.7826;MLEAC=2;MLEAF=1.00;MQ=49.42;MQ0=1;QD=29.97;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1845,144,0
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1045 chr1 42038 . G T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.265;DP=49;Dels=0.00;FS=6.121;HaplotypeScore=5.5713;MLEAC=1;MLEAF=0.500;MQ=49.15;MQ0=1;MQRankSum=2.868;QD=10.28;ReadPosRankSum=0.582;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:532,0,906
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1046 chr1 42046 . G A 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.504;DP=52;Dels=0.00;FS=2.418;HaplotypeScore=4.5717;MLEAC=1;MLEAF=0.500;MQ=49.00;MQ0=1;MQRankSum=-3.243;QD=17.82;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:955,0,706
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1047 chr1 42061 . C T 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.775;DP=49;Dels=0.00;FS=5.764;HaplotypeScore=4.9754;MLEAC=1;MLEAF=0.500;MQ=48.97;MQ0=1;MQRankSum=3.673;QD=14.79;ReadPosRankSum=0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:753,0,792
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1048 chr1 42071 . C T 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.982;DP=45;Dels=0.00;FS=4.388;HaplotypeScore=4.7774;MLEAC=1;MLEAF=0.500;MQ=49.26;MQ0=1;MQRankSum=-4.302;QD=15.22;ReadPosRankSum=-0.554;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:713,0,676
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1049 chr1 42082 . T C 1927.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=49.55;MQ0=1;QD=25.16;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:1956,150,0
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1050 chr1 42083 . G T 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.128;DP=49;Dels=0.00;FS=4.144;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=49.42;MQ0=1;MQRankSum=-4.087;QD=13.97;ReadPosRankSum=1.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:713,0,858
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1051 chr1 42106 . A G 1999.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.98;MQ0=2;QD=36.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2028,156,0
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1052 chr1 42149 . T C 1779.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.012;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=10.4982;MLEAC=2;MLEAF=1.00;MQ=39.34;MQ0=6;MQRankSum=2.932;QD=26.56;ReadPosRankSum=0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:9,58:67:99:1808,122,0
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1053 chr1 42196 . C T 798.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.783;DP=73;Dels=0.00;FS=15.517;HaplotypeScore=23.7489;MLEAC=1;MLEAF=0.500;MQ=35.03;MQ0=7;MQRankSum=3.313;QD=10.94;ReadPosRankSum=0.091;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,28:73:99:827,0,820
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1054 chr1 42202 . T C 1564.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.114;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=23.7489;MLEAC=2;MLEAF=1.00;MQ=32.75;MQ0=6;MQRankSum=3.687;QD=24.84;ReadPosRankSum=-0.517;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:8,55:63:99:1593,107,0
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1055 chr1 42204 . C T 644.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.569;DP=62;Dels=0.00;FS=14.833;HaplotypeScore=23.7489;MLEAC=1;MLEAF=0.500;MQ=32.93;MQ0=6;MQRankSum=3.649;QD=10.40;ReadPosRankSum=1.585;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,23:62:99:673,0,666
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1056 chr1 42208 . C T 643.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.545;DP=62;Dels=0.00;FS=14.833;HaplotypeScore=19.1747;MLEAC=1;MLEAF=0.500;MQ=32.93;MQ0=6;MQRankSum=3.599;QD=10.38;ReadPosRankSum=2.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,23:62:99:672,0,666
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1057 chr1 42212 . T A 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.097;DP=60;Dels=0.00;FS=12.104;HaplotypeScore=19.4395;MLEAC=1;MLEAF=0.500;MQ=33.30;MQ0=6;MQRankSum=3.512;QD=10.15;ReadPosRankSum=2.280;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,22:60:99:637,0,656
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1058 chr1 42218 . A G 1530.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.638;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=8.9344;MLEAC=2;MLEAF=1.00;MQ=32.94;MQ0=6;MQRankSum=-0.881;QD=24.30;ReadPosRankSum=-1.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,62:63:93:1559,93,0
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1059 chr1 42221 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.038;DP=65;Dels=0.00;FS=5.554;HaplotypeScore=8.9344;MLEAC=1;MLEAF=0.500;MQ=33.39;MQ0=6;MQRankSum=-1.189;QD=9.63;ReadPosRankSum=0.529;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,30:65:99:654,0,793
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1060 chr1 42234 . A G 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.221;DP=52;Dels=0.00;FS=7.954;HaplotypeScore=4.3119;MLEAC=1;MLEAF=0.500;MQ=36.56;MQ0=1;MQRankSum=-1.940;QD=11.46;ReadPosRankSum=0.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:624,0,788
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1061 chr1 42260 . T C 375.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.178;DP=42;Dels=0.00;FS=4.638;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=36.16;MQ0=0;MQRankSum=-1.412;QD=8.95;ReadPosRankSum=0.401;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:404,0,716
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1062 chr1 42263 . G A 538.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.843;DP=37;Dels=0.00;FS=4.803;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=35.87;MQ0=0;MQRankSum=0.904;QD=14.56;ReadPosRankSum=0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:567,0,421
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1063 chr1 42280 . G A 383.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.383;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=36.50;MQ0=2;MQRankSum=0.805;QD=9.84;ReadPosRankSum=2.659;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:412,0,542
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|
1064 chr1 42294 . C T 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.243;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=36.41;MQ0=2;MQRankSum=-0.883;QD=11.65;ReadPosRankSum=-0.558;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:436,0,494
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|
1065 chr1 42305 . C T 1338.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.50;MQ0=2;QD=33.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1367,111,0
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|
|
1066 chr1 42316 . T C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.870;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=38.47;MQ0=2;MQRankSum=-1.556;QD=10.46;ReadPosRankSum=-0.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:457,0,721
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|
|
1067 chr1 42344 . C T 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.289;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.7128;MLEAC=1;MLEAF=0.500;MQ=39.55;MQ0=2;MQRankSum=1.059;QD=16.22;ReadPosRankSum=1.851;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:823,0,592
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|
|
1068 chr1 42360 . A G 1733.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.46;MQ0=1;QD=34.68;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1762,141,0
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1069 chr1 42373 . G A 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.78;MQ0=0;MQRankSum=-1.866;QD=13.38;ReadPosRankSum=-0.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:657,0,768
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|
1070 chr1 42400 . A C 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.520;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=4.7967;MLEAC=1;MLEAF=0.500;MQ=44.88;MQ0=0;MQRankSum=-2.723;QD=12.16;ReadPosRankSum=1.372;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:612,0,919
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|
|
1071 chr1 42416 . C T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.458;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=3.7990;MLEAC=1;MLEAF=0.500;MQ=44.11;MQ0=0;MQRankSum=2.735;QD=16.06;ReadPosRankSum=-0.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:735,0,601
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|
1072 chr1 42478 . C T 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.823;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=34.32;MQ0=1;MQRankSum=-2.431;QD=5.99;ReadPosRankSum=1.216;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:11,10:21:99:154,0,359
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|
1073 chr1 42479 . A G 606.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.75;MQ0=1;QD=27.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,22:22:54:635,54,0
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1074 chr1 42486 . A G 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.373;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=32.44;MQ0=2;MQRankSum=-2.500;QD=6.25;ReadPosRankSum=0.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:11,12:23:99:172,0,350
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1075 chr1 42503 . T A 579.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.98;MQ0=2;QD=25.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,23:23:51:608,51,0
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1076 chr1 42535 . G A 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.561;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.4516;MLEAC=1;MLEAF=0.500;MQ=39.57;MQ0=2;MQRankSum=-1.226;QD=12.17;ReadPosRankSum=-0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,18:33:99:430,0,463
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1077 chr1 42539 . G A 442.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.544;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.4516;MLEAC=1;MLEAF=0.500;MQ=39.57;MQ0=2;MQRankSum=-1.381;QD=13.42;ReadPosRankSum=-0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,19:33:99:471,0,422
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1078 chr1 42553 . C T 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.604;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=39.64;MQ0=2;MQRankSum=0.155;QD=15.72;ReadPosRankSum=-1.432;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,18:36:99:594,0,398
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1079 chr1 42568 . A G 1099.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9332;MLEAC=2;MLEAF=1.00;MQ=40.82;MQ0=1;QD=33.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:87:1128,87,0
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1080 chr1 42617 . A T 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.148;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.50;MQ0=1;MQRankSum=0.049;QD=7.30;ReadPosRankSum=-1.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,9:29:99:240,0,633
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1081 chr1 42618 . A G 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.495;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.87;MQ0=1;MQRankSum=-0.029;QD=7.03;ReadPosRankSum=-1.252;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:211,0,532
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1082 chr1 42641 . A G 782.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.347;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=2.7330;MLEAC=2;MLEAF=1.00;MQ=36.44;MQ0=2;MQRankSum=1.595;QD=28.99;ReadPosRankSum=1.317;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:2,25:27:63:811,63,0
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1083 chr1 42646 . G A 734.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.828;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=2.7330;MLEAC=2;MLEAF=1.00;MQ=36.88;MQ0=1;MQRankSum=1.306;QD=29.39;ReadPosRankSum=1.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:2,23:25:60:763,60,0
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1084 chr1 42650 . A G 144.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DP=22;Dels=0.00;FS=1.719;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=37.75;MQ0=1;MQRankSum=-2.354;QD=6.58;ReadPosRankSum=1.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,9:22:99:173,0,443
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1085 chr1 42661 . T C 766.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.02;MQ0=1;QD=31.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,24:24:63:795,63,0
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1086 chr1 42680 . G T 412.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.405;DP=23;Dels=0.00;FS=1.837;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.36;MQ0=1;MQRankSum=-0.922;QD=17.95;ReadPosRankSum=-0.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:6,17:23:99:441,0,171
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1087 chr1 42698 . A G 779.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.880;DP=34;Dels=0.00;FS=3.589;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=48.79;MQ0=1;MQRankSum=-0.707;QD=22.93;ReadPosRankSum=1.071;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:9,25:34:99:808,0,202
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1088 chr1 42700 . C T 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.444;DP=35;Dels=0.00;FS=3.712;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=49.15;MQ0=1;MQRankSum=0.156;QD=5.31;ReadPosRankSum=-1.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,9:35:99:214,0,848
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1089 chr1 42716 . C A 1242.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=51.83;MQ0=0;QD=25.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,34:34:96:1271,96,0
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1090 chr1 42723 . C T 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.200;DP=39;Dels=0.00;FS=3.206;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.95;MQ0=0;MQRankSum=1.358;QD=5.20;ReadPosRankSum=-2.013;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,11:39:99:231,0,953
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1091 chr1 42738 . G A 1423.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=54.09;MQ0=0;QD=27.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1452,108,0
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1092 chr1 42747 . C T 806.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.256;DP=38;Dels=0.00;FS=1.475;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=55.27;MQ0=0;MQRankSum=-1.468;QD=21.23;ReadPosRankSum=1.165;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:835,0,401
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1093 chr1 42749 . C T 342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.407;DP=38;Dels=0.00;FS=1.475;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=55.27;MQ0=0;MQRankSum=2.557;QD=9.02;ReadPosRankSum=-1.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:371,0,833
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1094 chr1 42815 . T C 1223.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.80;MQ0=1;QD=33.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,37:37:96:1252,96,0
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1095 chr1 42840 . A G 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.801;DP=40;Dels=0.00;FS=1.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.73;MQ0=1;MQRankSum=0.745;QD=14.59;ReadPosRankSum=1.278;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:612,0,601
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1096 chr1 42845 . A G 575.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=39;Dels=0.00;FS=1.210;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.65;MQ0=1;MQRankSum=0.482;QD=14.76;ReadPosRankSum=1.710;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:604,0,571
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1097 chr1 42846 . G A 1308.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.65;MQ0=1;QD=33.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1337,102,0
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1098 chr1 42848 . G A 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.965;DP=41;Dels=0.00;FS=1.189;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.81;MQ0=1;MQRankSum=0.720;QD=14.29;ReadPosRankSum=1.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:614,0,573
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1099 chr1 42865 . C T 339.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.192;DP=50;Dels=0.00;FS=4.589;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=57.49;MQ0=1;MQRankSum=-0.645;QD=6.80;ReadPosRankSum=1.619;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,14:50:99:368,0,1156
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1100 chr1 42867 . G A 292.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.267;DP=50;Dels=0.00;FS=2.949;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=57.49;MQ0=1;MQRankSum=-0.500;QD=5.86;ReadPosRankSum=1.965;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,13:50:99:321,0,1202
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1101 chr1 42868 . T C 1723.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9989;MLEAC=2;MLEAF=1.00;MQ=57.44;MQ0=1;QD=31.13;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1752,135,0
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1102 chr1 42872 . C T 1168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.083;DP=49;Dels=0.00;FS=2.969;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=57.44;MQ0=1;MQRankSum=0.821;QD=23.85;ReadPosRankSum=-1.131;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,36:49:99:1197,0,340
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1103 chr1 42885 . T C 1721.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.922;DP=50;Dels=0.00;FS=3.297;HaplotypeScore=2.9991;MLEAC=2;MLEAF=1.00;MQ=57.48;MQ0=2;MQRankSum=-0.479;QD=34.44;ReadPosRankSum=1.511;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,48:50:99:1750,100,0
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1104 chr1 42886 . C T 1072.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.810;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=57.48;MQ0=2;MQRankSum=1.039;QD=21.46;ReadPosRankSum=1.761;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,32:50:99:1101,0,484
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1105 chr1 42890 . G T 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.510;DP=56;Dels=0.00;FS=1.156;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=57.75;MQ0=2;MQRankSum=-0.672;QD=7.39;ReadPosRankSum=-1.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,18:56:99:442,0,1293
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1106 chr1 42926 . C T 1188.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.287;DP=58;Dels=0.00;FS=7.798;HaplotypeScore=2.7439;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=1;MQRankSum=-0.975;QD=20.50;ReadPosRankSum=0.418;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,35:58:99:1217,0,729
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1107 chr1 42931 . T C 2121.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=2.7439;MLEAC=2;MLEAF=1.00;MQ=59.00;MQ0=1;QD=32.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2150,163,0
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1108 chr1 42980 . T C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.396;DP=47;Dels=0.00;FS=6.054;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-0.991;QD=18.08;ReadPosRankSum=1.098;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,25:47:99:878,0,734
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1109 chr1 43004 . A G 1350.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.45;MQ0=0;QD=34.40;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1379,105,0
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1110 chr1 43009 . G A 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.395;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.02;MQ0=0;MQRankSum=2.090;QD=14.47;ReadPosRankSum=0.512;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:578,0,652
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1111 chr1 43016 . A G 1291.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.56;MQ0=0;QD=26.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1320,99,0
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1112 chr1 43030 . G A 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.190;DP=40;Dels=0.00;FS=1.252;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.04;MQ0=0;MQRankSum=-2.465;QD=14.89;ReadPosRankSum=-0.325;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:624,0,708
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1113 chr1 43039 . G A 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.020;DP=38;Dels=0.00;FS=2.920;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.44;MQ0=0;MQRankSum=-1.493;QD=12.99;ReadPosRankSum=0.606;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:522,0,755
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1114 chr1 43040 . G A 554.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.177;DP=40;Dels=0.00;FS=4.756;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.41;MQ0=0;MQRankSum=-1.155;QD=13.87;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,18:40:99:583,0,758
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1115 chr1 43050 . T C 1807.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.22;MQ0=0;QD=26.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1836,141,0
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1116 chr1 43061 . T A 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.626;DP=49;Dels=0.00;FS=4.322;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.00;MQ0=0;MQRankSum=1.606;QD=17.65;ReadPosRankSum=1.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,28:49:99:893,0,625
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1117 chr1 43067 . C T 855.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.160;DP=51;Dels=0.00;FS=4.058;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=0;MQRankSum=-0.462;QD=16.78;ReadPosRankSum=2.101;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:884,0,760
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1118 chr1 43068 . G T 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.560;DP=53;Dels=0.00;FS=5.783;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=52.75;MQ0=0;MQRankSum=2.286;QD=16.58;ReadPosRankSum=2.073;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,27:53:99:907,0,821
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1119 chr1 43083 . G C 2208.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.92;MQ0=0;QD=33.11;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2237,169,0
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1120 chr1 43097 . T C 2191.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.07;MQ0=0;QD=28.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,56:57:99:2220,166,0
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1121 chr1 43150 . T A 998.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.009;DP=54;Dels=0.00;FS=2.461;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.65;MQ0=0;MQRankSum=1.401;QD=18.50;ReadPosRankSum=-1.279;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,30:54:99:1027,0,700
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1122 chr1 43153 . G A 1106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.471;DP=58;Dels=0.00;FS=3.788;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=45.16;MQ0=0;MQRankSum=1.366;QD=19.08;ReadPosRankSum=-1.696;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1135,0,730
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1123 chr1 43183 . T C 1947.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.34;MQ0=0;QD=33.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1976,147,0
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1124 chr1 43187 . G A 720.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.656;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=4.9656;MLEAC=1;MLEAF=0.500;MQ=48.85;MQ0=0;MQRankSum=-0.333;QD=14.13;ReadPosRankSum=0.219;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:749,0,974
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1125 chr1 43195 . A G 2077.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.472;DP=56;Dels=0.00;FS=5.362;HaplotypeScore=4.9656;MLEAC=2;MLEAF=1.00;MQ=50.45;MQ0=0;MQRankSum=0.283;QD=34.04;ReadPosRankSum=1.669;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,54:56:99:2106,123,0
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1126 chr1 43197 . G A 1062.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.305;DP=58;Dels=0.00;FS=1.101;HaplotypeScore=4.9656;MLEAC=1;MLEAF=0.500;MQ=50.81;MQ0=0;MQRankSum=0.868;QD=18.32;ReadPosRankSum=0.524;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,32:58:99:1091,0,879
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1127 chr1 43231 . C A 699.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.226;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.98;MQ0=0;MQRankSum=-0.040;QD=12.06;ReadPosRankSum=0.473;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,22:58:99:728,0,1277
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1128 chr1 43246 . T C 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.141;DP=72;Dels=0.00;FS=7.335;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=53.67;MQ0=0;MQRankSum=-3.808;QD=0.61;ReadPosRankSum=-2.768;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,8:72:72:72,0,2204
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1129 chr1 43265 . A T 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.501;DP=75;Dels=0.00;FS=7.472;HaplotypeScore=3.7546;MLEAC=1;MLEAF=0.500;MQ=52.35;MQ0=0;MQRankSum=-3.233;QD=0.44;ReadPosRankSum=-2.359;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,7:75:61:61,0,2183
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1130 chr1 43276 . G A 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.432;DP=69;Dels=0.00;FS=3.775;HaplotypeScore=9.7497;MLEAC=1;MLEAF=0.500;MQ=52.79;MQ0=0;MQRankSum=-3.715;QD=1.13;ReadPosRankSum=1.470;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,9:69:99:106,0,2099
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1131 chr1 43278 . T C 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.807;DP=70;Dels=0.00;FS=18.468;HaplotypeScore=9.7497;MLEAC=1;MLEAF=0.500;MQ=52.72;MQ0=0;MQRankSum=-6.081;QD=5.05;ReadPosRankSum=2.009;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,18:70:99:382,0,1868
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1132 chr1 43282 . A G 2155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.741;DP=72;Dels=0.00;FS=5.810;HaplotypeScore=18.7776;MLEAC=1;MLEAF=0.500;MQ=51.85;MQ0=0;MQRankSum=3.314;QD=29.94;ReadPosRankSum=-2.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:10,62:72:99:2184,0,134
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1133 chr1 43285 . G A 103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.628;DP=73;Dels=0.00;FS=5.951;HaplotypeScore=50.5662;MLEAC=1;MLEAF=0.500;MQ=51.51;MQ0=0;MQRankSum=-3.088;QD=1.42;ReadPosRankSum=2.735;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,10:73:99:132,0,2235
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1134 chr1 43291 . C G 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.349;DP=74;Dels=0.00;FS=19.101;HaplotypeScore=33.7389;MLEAC=1;MLEAF=0.500;MQ=51.06;MQ0=1;MQRankSum=-3.986;QD=2.73;ReadPosRankSum=0.439;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,11:74:99:230,0,2102
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1135 chr1 43293 . A T 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.021;DP=71;Dels=0.00;FS=10.885;HaplotypeScore=23.8257;MLEAC=1;MLEAF=0.500;MQ=50.40;MQ0=1;MQRankSum=-3.987;QD=2.73;ReadPosRankSum=2.507;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,14:71:99:222,0,1937
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1136 chr1 43298 . C T 2572.77 . AC=2;AF=1.00;AN=2;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=13.9125;MLEAC=2;MLEAF=1.00;MQ=49.91;MQ0=1;QD=27.53;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,69:69:99:2601,199,0
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1137 chr1 43315 . A C 2446.77 . AC=2;AF=1.00;AN=2;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.64;MQ0=1;QD=24.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,67:67:99:2475,196,0
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1138 chr1 43326 . A T 2504.77 . AC=2;AF=1.00;AN=2;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=25.9658;MLEAC=2;MLEAF=1.00;MQ=48.61;MQ0=1;QD=28.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,68:68:99:2533,196,0
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1139 chr1 43328 . C G 281.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.840;DP=70;Dels=0.00;FS=18.175;HaplotypeScore=28.9637;MLEAC=1;MLEAF=0.500;MQ=48.83;MQ0=1;MQRankSum=-1.433;QD=4.03;ReadPosRankSum=-2.248;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:54,16:70:99:310,0,1933
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1140 chr1 43332 . G C 378.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.653;DP=68;Dels=0.00;FS=31.387;HaplotypeScore=27.9641;MLEAC=1;MLEAF=0.500;MQ=48.56;MQ0=2;MQRankSum=3.076;QD=5.57;ReadPosRankSum=0.704;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,15:68:99:407,0,1696
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1141 chr1 43333 . C T 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.715;DP=63;Dels=0.00;FS=24.273;HaplotypeScore=25.9652;MLEAC=1;MLEAF=0.500;MQ=48.61;MQ0=2;MQRankSum=-3.220;QD=4.08;ReadPosRankSum=0.717;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,12:63:99:285,0,1646
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1142 chr1 43371 . C T 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.139;DP=73;Dels=0.00;FS=22.148;HaplotypeScore=6.9922;MLEAC=1;MLEAF=0.500;MQ=51.66;MQ0=2;MQRankSum=2.809;QD=6.64;ReadPosRankSum=-0.324;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,18:73:99:513,0,1764
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1143 chr1 43372 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.403;DP=74;Dels=0.00;FS=22.148;HaplotypeScore=6.9922;MLEAC=1;MLEAF=0.500;MQ=51.31;MQ0=3;MQRankSum=2.584;QD=6.60;ReadPosRankSum=-0.403;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,18:74:99:517,0,1762
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1144 chr1 43392 . C T 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.597;DP=82;Dels=0.00;FS=11.173;HaplotypeScore=1.9978;MLEAC=1;MLEAF=0.500;MQ=51.96;MQ0=2;MQRankSum=3.354;QD=9.66;ReadPosRankSum=0.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,27:82:99:820,0,1545
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1145 chr1 43419 . G A 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.314;DP=85;Dels=0.00;FS=4.704;HaplotypeScore=41.2098;MLEAC=1;MLEAF=0.500;MQ=52.49;MQ0=2;MQRankSum=-3.922;QD=0.80;ReadPosRankSum=-1.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,15:85:96:96,0,2450
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1146 chr1 43420 . T C 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.822;DP=85;Dels=0.00;FS=8.730;HaplotypeScore=41.2098;MLEAC=1;MLEAF=0.500;MQ=52.49;MQ0=2;MQRankSum=-3.994;QD=1.48;ReadPosRankSum=-1.438;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,17:85:99:154,0,2361
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1147 chr1 43424 . C T 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.398;DP=86;Dels=0.00;FS=5.028;HaplotypeScore=83.0946;MLEAC=1;MLEAF=0.500;MQ=52.08;MQ0=2;MQRankSum=2.883;QD=9.25;ReadPosRankSum=2.423;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,27:86:99:824,0,1702
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1148 chr1 43442 . C T 207.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;DP=81;Dels=0.00;FS=4.587;HaplotypeScore=5.9982;MLEAC=1;MLEAF=0.500;MQ=51.64;MQ0=1;MQRankSum=-5.183;QD=2.57;ReadPosRankSum=1.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,18:81:99:236,0,2162
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1149 chr1 43464 . T C 1004.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.733;DP=83;Dels=0.00;FS=6.657;HaplotypeScore=7.8783;MLEAC=1;MLEAF=0.500;MQ=51.04;MQ0=2;MQRankSum=-7.377;QD=12.11;ReadPosRankSum=-0.440;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,40:83:99:1033,0,1434
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1150 chr1 43478 . C T 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.768;DP=78;Dels=0.00;FS=2.728;HaplotypeScore=27.3493;MLEAC=1;MLEAF=0.500;MQ=50.85;MQ0=1;MQRankSum=-1.601;QD=4.14;ReadPosRankSum=-1.498;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,15:78:99:351,0,2012
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1151 chr1 43479 . T C 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.824;DP=78;Dels=0.00;FS=7.130;HaplotypeScore=27.3493;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=1;MQRankSum=-1.781;QD=0.23;ReadPosRankSum=0.470;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,8:78:46:46,0,2305
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1152 chr1 43500 . C G 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.139;DP=75;Dels=0.00;FS=9.744;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.12;MQ0=1;MQRankSum=3.454;QD=2.78;ReadPosRankSum=-0.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,12:75:99:237,0,2108
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1153 chr1 43510 . A G 135.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=78;Dels=0.00;FS=13.593;HaplotypeScore=39.7676;MLEAC=1;MLEAF=0.500;MQ=48.31;MQ0=1;MQRankSum=3.326;QD=1.74;ReadPosRankSum=-1.053;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,10:78:99:164,0,2251
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1154 chr1 43512 . T C 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=79;Dels=0.00;FS=5.766;HaplotypeScore=29.7717;MLEAC=1;MLEAF=0.500;MQ=48.16;MQ0=1;MQRankSum=-2.674;QD=5.09;ReadPosRankSum=-1.477;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,18:79:99:430,0,1984
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|
|
1155 chr1 43517 . T C 72.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.078;DP=74;Dels=0.00;FS=7.633;HaplotypeScore=48.4896;MLEAC=1;MLEAF=0.500;MQ=47.06;MQ0=1;MQRankSum=-2.543;QD=0.98;ReadPosRankSum=0.457;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,11:74:99:101,0,2153
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|
1156 chr1 43520 . C A 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.233;DP=74;Dels=0.00;FS=3.451;HaplotypeScore=48.4896;MLEAC=1;MLEAF=0.500;MQ=46.48;MQ0=1;MQRankSum=-2.123;QD=0.54;ReadPosRankSum=0.579;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,10:74:68:68,0,2205
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|
1157 chr1 43523 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=77;Dels=0.00;FS=9.238;HaplotypeScore=43.3257;MLEAC=1;MLEAF=0.500;MQ=45.89;MQ0=1;MQRankSum=2.335;QD=0.44;ReadPosRankSum=-0.952;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,7:77:62:62,0,2240
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1158 chr1 43525 . A G 330.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.632;DP=75;Dels=0.00;FS=2.429;HaplotypeScore=41.3363;MLEAC=1;MLEAF=0.500;MQ=46.07;MQ0=1;MQRankSum=2.219;QD=4.41;ReadPosRankSum=0.363;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,15:75:99:359,0,1931
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1159 chr1 43532 . C T 638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=73;Dels=0.00;FS=11.099;HaplotypeScore=23.1272;MLEAC=1;MLEAF=0.500;MQ=45.27;MQ0=2;MQRankSum=1.051;QD=8.75;ReadPosRankSum=-0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,24:73:99:667,0,1489
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|
|
1160 chr1 43535 . C G 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.745;DP=71;Dels=0.00;FS=13.340;HaplotypeScore=30.0213;MLEAC=1;MLEAF=0.500;MQ=44.73;MQ0=2;MQRankSum=1.228;QD=8.70;ReadPosRankSum=-0.541;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,24:71:99:646,0,1479
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1161 chr1 43544 . G A 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.191;DP=67;Dels=0.00;FS=8.590;HaplotypeScore=21.3628;MLEAC=1;MLEAF=0.500;MQ=43.73;MQ0=2;MQRankSum=-0.099;QD=12.70;ReadPosRankSum=1.165;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,30:67:99:879,0,1032
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|
|
1162 chr1 43548 . T C 2142.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=18.0294;MLEAC=2;MLEAF=1.00;MQ=43.48;MQ0=1;QD=34.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2171,171,0
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1163 chr1 43554 . A G 1643.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=19.3162;MLEAC=2;MLEAF=1.00;MQ=40.15;MQ0=1;QD=32.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1672,135,0
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|
|
1164 chr1 43556 . A T 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.542;DP=50;Dels=0.00;FS=20.048;HaplotypeScore=10.4239;MLEAC=1;MLEAF=0.500;MQ=40.15;MQ0=1;MQRankSum=1.405;QD=6.36;ReadPosRankSum=-0.232;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:346,0,981
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|
1165 chr1 43562 . A C 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.681;DP=50;Dels=0.00;FS=14.927;HaplotypeScore=31.3082;MLEAC=1;MLEAF=0.500;MQ=40.43;MQ0=1;MQRankSum=1.421;QD=7.74;ReadPosRankSum=-0.683;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,16:50:99:415,0,1027
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|
1166 chr1 43569 . T C 1156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.578;DP=43;Dels=0.00;FS=13.268;HaplotypeScore=30.7711;MLEAC=1;MLEAF=0.500;MQ=39.33;MQ0=1;MQRankSum=-1.864;QD=26.90;ReadPosRankSum=1.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:4,39:43:35:1185,0,35
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|
1167 chr1 43571 . A G 1091.86 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=32.6687;MLEAC=1;MLEAF=0.500;MQ=38.46;MQ0=1;QD=25.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,36:43:99:1234,99,0
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1168 chr1 43572 . A G 286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.687;DP=45;Dels=0.00;FS=3.225;HaplotypeScore=32.6687;MLEAC=1;MLEAF=0.500;MQ=37.69;MQ0=2;MQRankSum=-0.039;QD=6.37;ReadPosRankSum=0.842;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:315,0,750
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1169 chr1 43594 . C T 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.410;DP=44;Dels=0.00;FS=5.674;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=35.55;MQ0=2;MQRankSum=0.307;QD=3.77;ReadPosRankSum=0.092;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,10:44:99:194,0,793
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1170 chr1 43610 . C T 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.339;DP=33;Dels=0.00;FS=6.419;HaplotypeScore=4.5214;MLEAC=1;MLEAF=0.500;MQ=33.96;MQ0=2;MQRankSum=-0.609;QD=3.30;ReadPosRankSum=-0.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,8:33:99:137,0,510
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1171 chr1 43619 . T C 412.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=5.3349;MLEAC=2;MLEAF=1.00;MQ=30.87;MQ0=2;QD=17.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,23:23:36:441,36,0
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1172 chr1 43627 . T G 140.9 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.23;MQ0=1;QD=9.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,15:15:15:169,15,0
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|
1173 chr1 43635 . C T 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.559;DP=28;Dels=0.00;FS=10.098;HaplotypeScore=6.9461;MLEAC=1;MLEAF=0.500;MQ=36.02;MQ0=1;MQRankSum=-0.717;QD=0.64;ReadPosRankSum=-1.945;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,4:28:46:46,0,498
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1174 chr1 43639 . C T 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.381;DP=28;Dels=0.00;FS=3.565;HaplotypeScore=6.9461;MLEAC=1;MLEAF=0.500;MQ=36.02;MQ0=1;MQRankSum=-1.029;QD=4.46;ReadPosRankSum=0.326;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,10:28:99:153,0,405
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1175 chr1 43643 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=13.8923;MLEAC=1;MLEAF=0.500;MQ=36.79;MQ0=1;MQRankSum=0.952;QD=1.16;ReadPosRankSum=-1.543;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,5:29:62:62,0,530
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1176 chr1 43651 . G A 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.370;DP=33;Dels=0.00;FS=1.393;HaplotypeScore=3.9569;MLEAC=1;MLEAF=0.500;MQ=39.46;MQ0=1;MQRankSum=1.499;QD=7.78;ReadPosRankSum=1.421;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:285,0,426
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|
1177 chr1 43662 . C T 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.298;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=6.2383;MLEAC=1;MLEAF=0.500;MQ=44.29;MQ0=0;MQRankSum=0.474;QD=3.35;ReadPosRankSum=-0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,6:37:99:152,0,768
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1178 chr1 43664 . A G 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.800;DP=36;Dels=0.00;FS=5.877;HaplotypeScore=6.2383;MLEAC=1;MLEAF=0.500;MQ=45.71;MQ0=0;MQRankSum=-2.505;QD=4.72;ReadPosRankSum=-0.124;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,11:36:99:198,0,750
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1179 chr1 43668 . C T 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.039;DP=39;Dels=0.00;FS=8.049;HaplotypeScore=10.2065;MLEAC=1;MLEAF=0.500;MQ=45.43;MQ0=0;MQRankSum=-2.825;QD=7.71;ReadPosRankSum=-0.922;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:329,0,752
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1180 chr1 43678 . T A 200.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.531;DP=52;Dels=0.00;FS=11.972;HaplotypeScore=19.6024;MLEAC=1;MLEAF=0.500;MQ=44.28;MQ0=0;MQRankSum=-1.814;QD=3.86;ReadPosRankSum=1.661;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,12:52:99:229,0,1169
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1181 chr1 43686 . T C 1665.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=13.0300;MLEAC=2;MLEAF=1.00;MQ=44.10;MQ0=0;QD=29.75;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:1694,138,0
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1182 chr1 43688 . C T 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.410;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=30.3912;MLEAC=1;MLEAF=0.500;MQ=43.92;MQ0=0;MQRankSum=4.253;QD=8.54;ReadPosRankSum=1.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,17:55:99:498,0,1002
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|
1183 chr1 43698 . T C 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.598;DP=67;Dels=0.00;FS=8.840;HaplotypeScore=47.7369;MLEAC=1;MLEAF=0.500;MQ=45.08;MQ0=0;MQRankSum=-4.239;QD=8.07;ReadPosRankSum=-0.495;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,26:67:99:569,0,1255
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1184 chr1 43705 . C T 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.077;DP=69;Dels=0.00;FS=3.045;HaplotypeScore=32.6622;MLEAC=1;MLEAF=0.500;MQ=45.16;MQ0=0;MQRankSum=-0.571;QD=2.33;ReadPosRankSum=0.145;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,10:69:99:189,0,1720
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1185 chr1 43713 . A C 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.553;DP=77;Dels=0.00;FS=11.201;HaplotypeScore=42.6440;MLEAC=1;MLEAF=0.500;MQ=45.67;MQ0=0;MQRankSum=-5.163;QD=8.23;ReadPosRankSum=0.667;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,32:77:99:662,0,1440
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1186 chr1 43719 . A T 122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.822;DP=81;Dels=0.00;FS=4.781;HaplotypeScore=21.7031;MLEAC=1;MLEAF=0.500;MQ=45.82;MQ0=0;MQRankSum=-0.691;QD=1.52;ReadPosRankSum=-0.778;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,10:81:99:151,0,2102
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1187 chr1 43742 . A T 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.288;DP=82;Dels=0.00;FS=35.671;HaplotypeScore=38.7529;MLEAC=1;MLEAF=0.500;MQ=46.28;MQ0=0;MQRankSum=1.619;QD=4.07;ReadPosRankSum=-0.708;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,15:82:99:362,0,1988
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1188 chr1 43754 . G A 395.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.834;DP=81;Dels=0.00;FS=11.585;HaplotypeScore=3.8103;MLEAC=1;MLEAF=0.500;MQ=45.89;MQ0=0;MQRankSum=-4.306;QD=4.89;ReadPosRankSum=0.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,22:81:99:424,0,1874
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1189 chr1 43755 . G A 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.388;DP=81;Dels=0.00;FS=11.585;HaplotypeScore=3.8103;MLEAC=1;MLEAF=0.500;MQ=45.89;MQ0=0;MQRankSum=-4.189;QD=4.47;ReadPosRankSum=0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,22:81:99:390,0,1864
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1190 chr1 43771 . C T 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.087;DP=84;Dels=0.00;FS=0.000;HaplotypeScore=17.4268;MLEAC=1;MLEAF=0.500;MQ=48.68;MQ0=0;MQRankSum=-0.578;QD=0.63;ReadPosRankSum=-0.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,9:84:81:81,0,2479
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1191 chr1 43781 . A C 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.186;DP=89;Dels=0.00;FS=0.000;HaplotypeScore=27.2915;MLEAC=1;MLEAF=0.500;MQ=50.47;MQ0=0;MQRankSum=-1.448;QD=1.76;ReadPosRankSum=-0.883;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,12:89:99:185,0,2613
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1192 chr1 43786 . G A 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.170;DP=84;Dels=0.00;FS=1.288;HaplotypeScore=17.3780;MLEAC=1;MLEAF=0.500;MQ=51.33;MQ0=0;MQRankSum=-1.617;QD=1.74;ReadPosRankSum=-0.901;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,12:84:99:174,0,2552
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1193 chr1 43806 . T C 1310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=35.5387;MLEAC=1;MLEAF=0.500;MQ=51.97;MQ0=0;MQRankSum=-6.251;QD=15.98;ReadPosRankSum=0.139;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,41:82:99:1339,0,1390
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1194 chr1 43810 . C T 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.203;DP=79;Dels=0.00;FS=10.312;HaplotypeScore=35.5390;MLEAC=1;MLEAF=0.500;MQ=52.20;MQ0=0;MQRankSum=-2.175;QD=1.48;ReadPosRankSum=1.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,10:79:99:145,0,2427
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1195 chr1 43816 . C T 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.428;DP=76;Dels=0.00;FS=1.622;HaplotypeScore=86.3319;MLEAC=1;MLEAF=0.500;MQ=52.70;MQ0=0;MQRankSum=-2.822;QD=2.44;ReadPosRankSum=1.394;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,11:76:99:214,0,1931
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1196 chr1 43818 . A G 2850.77 . AC=2;AF=1.00;AN=2;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=49.3811;MLEAC=2;MLEAF=1.00;MQ=52.68;MQ0=0;QD=33.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,74:75:99:2879,223,0
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1197 chr1 43821 . G A 375.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.751;DP=80;Dels=0.00;FS=3.003;HaplotypeScore=41.4503;MLEAC=1;MLEAF=0.500;MQ=52.13;MQ0=2;MQRankSum=-3.694;QD=4.70;ReadPosRankSum=0.476;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,16:80:99:404,0,2083
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1198 chr1 43823 . G A 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.997;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=47.4468;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=2;MQRankSum=3.459;QD=8.60;ReadPosRankSum=0.112;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,24:81:99:725,0,1844
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1199 chr1 43834 . A C 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.959;DP=87;Dels=0.00;FS=5.047;HaplotypeScore=27.3319;MLEAC=1;MLEAF=0.500;MQ=51.57;MQ0=2;MQRankSum=-6.863;QD=11.49;ReadPosRankSum=1.136;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,40:87:99:1028,0,1538
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1200 chr1 43840 . C T 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.139;DP=85;Dels=0.00;FS=1.532;HaplotypeScore=28.5959;MLEAC=1;MLEAF=0.500;MQ=51.00;MQ0=2;MQRankSum=-0.945;QD=1.09;ReadPosRankSum=-1.311;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,11:85:99:121,0,2480
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1201 chr1 43841 . G A 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.192;DP=88;Dels=0.00;FS=8.668;HaplotypeScore=28.5959;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=2;MQRankSum=-6.447;QD=6.87;ReadPosRankSum=1.228;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,30:88:99:633,0,2003
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1202 chr1 43851 . A G 3242.77 . AC=2;AF=1.00;AN=2;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=1.7273;MLEAC=2;MLEAF=1.00;MQ=50.57;MQ0=3;QD=29.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,92:92:99:3271,253,0
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1203 chr1 43863 . A G 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.312;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=54.7219;MLEAC=1;MLEAF=0.500;MQ=49.86;MQ0=3;MQRankSum=-4.540;QD=0.20;ReadPosRankSum=0.738;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:83,14:97:48:48,0,2773
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1204 chr1 43864 . G A 1049.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.505;DP=94;Dels=0.00;FS=1.845;HaplotypeScore=54.7219;MLEAC=1;MLEAF=0.500;MQ=49.56;MQ0=3;MQRankSum=3.253;QD=11.17;ReadPosRankSum=-0.144;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,34:94:99:1078,0,1669
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1205 chr1 43866 . G C 1601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.813;DP=89;Dels=0.00;FS=2.991;HaplotypeScore=55.7192;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=3;MQRankSum=6.796;QD=18.00;ReadPosRankSum=1.587;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,49:89:99:1630,0,963
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1206 chr1 43877 . T G 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.373;DP=82;Dels=0.00;FS=4.511;HaplotypeScore=22.6567;MLEAC=1;MLEAF=0.500;MQ=48.08;MQ0=3;MQRankSum=-6.816;QD=8.86;ReadPosRankSum=-0.734;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,34:82:99:755,0,1613
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1207 chr1 43880 . G A 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.208;DP=81;Dels=0.00;FS=3.784;HaplotypeScore=34.1328;MLEAC=1;MLEAF=0.500;MQ=47.59;MQ0=3;MQRankSum=4.821;QD=5.75;ReadPosRankSum=0.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,19:81:99:494,0,1845
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1208 chr1 43886 . A G 2779.77 . AC=2;AF=1.00;AN=2;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=36.7766;MLEAC=2;MLEAF=1.00;MQ=47.06;MQ0=3;QD=33.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,83:83:99:2808,223,0
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1209 chr1 43895 . A G 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.900;DP=84;Dels=0.00;FS=3.557;HaplotypeScore=5.7833;MLEAC=1;MLEAF=0.500;MQ=47.29;MQ0=3;MQRankSum=3.874;QD=6.95;ReadPosRankSum=-0.792;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,22:84:99:612,0,1874
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1210 chr1 43919 . C T 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.966;DP=90;Dels=0.00;FS=10.596;HaplotypeScore=31.8093;MLEAC=1;MLEAF=0.500;MQ=48.00;MQ0=3;MQRankSum=-3.047;QD=1.38;ReadPosRankSum=2.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,12:90:99:152,0,2472
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1211 chr1 43921 . C T 1119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.683;DP=89;Dels=0.00;FS=11.456;HaplotypeScore=31.8093;MLEAC=1;MLEAF=0.500;MQ=47.77;MQ0=3;MQRankSum=-0.291;QD=12.58;ReadPosRankSum=1.796;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,38:89:99:1148,0,1412
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1212 chr1 43929 . G C 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.254;DP=96;Dels=0.00;FS=0.861;HaplotypeScore=31.8093;MLEAC=1;MLEAF=0.500;MQ=47.78;MQ0=4;MQRankSum=4.123;QD=8.49;ReadPosRankSum=0.847;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,31:96:99:843,0,1928
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1213 chr1 43954 . G A 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.709;DP=98;Dels=0.00;FS=3.403;HaplotypeScore=31.4020;MLEAC=1;MLEAF=0.500;MQ=48.81;MQ0=3;MQRankSum=-1.940;QD=5.12;ReadPosRankSum=-1.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,25:98:99:530,0,2436
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1214 chr1 43958 . T C 1162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.883;DP=98;Dels=0.00;FS=0.772;HaplotypeScore=41.3969;MLEAC=1;MLEAF=0.500;MQ=49.49;MQ0=3;MQRankSum=-3.408;QD=11.86;ReadPosRankSum=0.154;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,42:98:99:1191,0,1753
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1215 chr1 43959 . T C 3463.77 . AC=2;AF=1.00;AN=2;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=41.4115;MLEAC=2;MLEAF=1.00;MQ=49.49;MQ0=3;QD=29.91;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,98:98:99:3492,268,0
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1216 chr1 43966 . G T 228.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.214;DP=107;Dels=0.00;FS=4.094;HaplotypeScore=60.8308;MLEAC=1;MLEAF=0.500;MQ=49.53;MQ0=3;MQRankSum=-0.729;QD=2.14;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,14:107:99:257,0,2992
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1217 chr1 43969 . G A 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.432;DP=107;Dels=0.00;FS=1.978;HaplotypeScore=35.1970;MLEAC=1;MLEAF=0.500;MQ=49.50;MQ0=3;MQRankSum=-2.173;QD=5.55;ReadPosRankSum=-0.469;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,27:107:99:622,0,2650
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1218 chr1 43976 . G A 279.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.740;DP=112;Dels=0.00;FS=3.944;HaplotypeScore=55.4395;MLEAC=1;MLEAF=0.500;MQ=49.60;MQ0=4;MQRankSum=-1.018;QD=2.50;ReadPosRankSum=-0.480;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,15:112:99:308,0,3072
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1219 chr1 43984 . G A 813.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.553;DP=118;Dels=0.00;FS=2.892;HaplotypeScore=75.9412;MLEAC=1;MLEAF=0.500;MQ=50.30;MQ0=4;MQRankSum=0.547;QD=6.90;ReadPosRankSum=-0.638;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,29:118:99:842,0,2830
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1220 chr1 43988 . A C 840.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.759;DP=116;Dels=0.00;FS=5.433;HaplotypeScore=43.4214;MLEAC=1;MLEAF=0.500;MQ=50.72;MQ0=4;MQRankSum=4.795;QD=7.25;ReadPosRankSum=-1.758;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,34:116:99:869,0,2451
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1221 chr1 44002 . A G 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.568;DP=116;Dels=0.00;FS=0.958;HaplotypeScore=39.4904;MLEAC=1;MLEAF=0.500;MQ=51.56;MQ0=3;MQRankSum=-2.313;QD=3.79;ReadPosRankSum=1.726;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,20:116:99:468,0,2935
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1222 chr1 44007 . T A 1436.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.367;DP=111;Dels=0.00;FS=6.411;HaplotypeScore=43.4892;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=3;MQRankSum=-6.177;QD=12.94;ReadPosRankSum=0.970;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,51:111:99:1465,0,1937
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1223 chr1 44026 . T C 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.135;DP=110;Dels=0.00;FS=0.000;HaplotypeScore=6.8459;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=1;MQRankSum=-3.383;QD=0.29;ReadPosRankSum=-0.605;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:98,12:110:60:60,0,3255
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1224 chr1 44060 . T C 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=84;Dels=0.00;FS=2.470;HaplotypeScore=22.4896;MLEAC=1;MLEAF=0.500;MQ=51.59;MQ0=1;MQRankSum=4.395;QD=5.53;ReadPosRankSum=0.493;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,20:84:99:493,0,2021
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1225 chr1 44069 . C A 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.048;DP=73;Dels=0.00;FS=3.136;HaplotypeScore=49.4176;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=1;MQRankSum=-5.204;QD=3.39;ReadPosRankSum=-0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,13:73:99:276,0,1726
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1226 chr1 44072 . T A 252.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.800;DP=71;Dels=0.00;FS=1.293;HaplotypeScore=23.4451;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=1;MQRankSum=-3.737;QD=3.56;ReadPosRankSum=-1.197;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,14:71:99:281,0,1830
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1227 chr1 44082 . C T 240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.299;DP=69;Dels=0.00;FS=10.437;HaplotypeScore=20.4044;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-3.783;QD=3.49;ReadPosRankSum=-1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,13:69:99:269,0,1813
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1228 chr1 44096 . C T 607.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=19.4892;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=0;MQRankSum=4.352;QD=10.13;ReadPosRankSum=1.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,20:60:99:636,0,1132
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1229 chr1 44099 . T G 1703.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=15.7767;MLEAC=2;MLEAF=1.00;MQ=55.58;MQ0=0;QD=29.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1732,132,0
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1230 chr1 44100 . A T 1683.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=13.9885;MLEAC=2;MLEAF=1.00;MQ=55.80;MQ0=0;QD=31.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1712,129,0
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1231 chr1 44102 . A C 93.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.658;DP=47;Dels=0.00;FS=10.637;HaplotypeScore=20.9826;MLEAC=1;MLEAF=0.500;MQ=55.51;MQ0=0;MQRankSum=-3.780;QD=2.00;ReadPosRankSum=1.539;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,7:47:99:122,0,1452
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1232 chr1 44103 . G A 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.493;DP=47;Dels=0.00;FS=10.637;HaplotypeScore=20.9826;MLEAC=1;MLEAF=0.500;MQ=55.51;MQ0=0;MQRankSum=-3.780;QD=2.14;ReadPosRankSum=1.539;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,7:47:99:129,0,1433
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1233 chr1 44111 . T A 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.249;DP=55;Dels=0.00;FS=2.927;HaplotypeScore=2.1550;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-4.824;QD=3.38;ReadPosRankSum=-0.961;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,13:55:99:214,0,1474
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1234 chr1 44117 . C T 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.191;DP=61;Dels=0.00;FS=5.158;HaplotypeScore=10.4916;MLEAC=1;MLEAF=0.500;MQ=52.01;MQ0=0;MQRankSum=-3.964;QD=2.88;ReadPosRankSum=0.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,12:61:99:204,0,1632
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1235 chr1 44120 . C T 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.479;DP=63;Dels=0.00;FS=5.124;HaplotypeScore=10.4916;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=0;MQRankSum=-4.000;QD=2.69;ReadPosRankSum=1.094;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,12:63:99:198,0,1749
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1236 chr1 44126 . T A 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.677;DP=63;Dels=0.00;FS=8.122;HaplotypeScore=17.4822;MLEAC=1;MLEAF=0.500;MQ=52.02;MQ0=0;MQRankSum=-4.789;QD=6.36;ReadPosRankSum=-1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,21:63:99:429,0,1420
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1237 chr1 44133 . C T 24.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.065;DP=64;Dels=0.00;FS=3.868;HaplotypeScore=13.3538;MLEAC=1;MLEAF=0.500;MQ=51.28;MQ0=0;MQRankSum=-2.947;QD=0.39;ReadPosRankSum=-2.323;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,7:64:53:53,0,1875
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1238 chr1 44145 . T A 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.048;DP=72;Dels=0.00;FS=14.645;HaplotypeScore=3.9967;MLEAC=1;MLEAF=0.500;MQ=50.27;MQ0=0;MQRankSum=-4.480;QD=6.77;ReadPosRankSum=2.170;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,22:72:99:516,0,1706
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1239 chr1 44157 . T C 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.780;DP=70;Dels=0.00;FS=5.275;HaplotypeScore=5.7502;MLEAC=1;MLEAF=0.500;MQ=49.89;MQ0=0;MQRankSum=-1.502;QD=1.11;ReadPosRankSum=2.392;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,10:70:99:106,0,2013
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1240 chr1 44177 . T C 545.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.835;DP=73;Dels=0.00;FS=7.693;HaplotypeScore=14.5600;MLEAC=1;MLEAF=0.500;MQ=49.07;MQ0=0;MQRankSum=0.080;QD=7.48;ReadPosRankSum=0.748;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,20:73:99:574,0,1711
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1241 chr1 44183 . T C 78.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.281;DP=73;Dels=0.00;FS=3.202;HaplotypeScore=50.8308;MLEAC=1;MLEAF=0.500;MQ=49.60;MQ0=0;MQRankSum=-1.131;QD=1.08;ReadPosRankSum=-0.425;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,10:73:99:107,0,2164
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1242 chr1 44188 . G T 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.234;DP=74;Dels=0.00;FS=14.435;HaplotypeScore=30.4305;MLEAC=1;MLEAF=0.500;MQ=48.97;MQ0=0;MQRankSum=-4.140;QD=6.90;ReadPosRankSum=-1.345;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,24:74:99:539,0,1696
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1243 chr1 44191 . C G 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.241;DP=78;Dels=0.00;FS=1.989;HaplotypeScore=30.4305;MLEAC=1;MLEAF=0.500;MQ=49.48;MQ0=0;MQRankSum=3.081;QD=11.29;ReadPosRankSum=1.210;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,29:78:99:909,0,1490
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1244 chr1 44202 . T C 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.192;DP=70;Dels=0.00;FS=18.949;HaplotypeScore=45.1512;MLEAC=1;MLEAF=0.500;MQ=50.32;MQ0=0;MQRankSum=-3.780;QD=4.45;ReadPosRankSum=-1.041;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,17:70:99:340,0,1880
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|
|
1245 chr1 44205 . T G 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.786;DP=71;Dels=0.00;FS=2.009;HaplotypeScore=52.8564;MLEAC=1;MLEAF=0.500;MQ=50.01;MQ0=0;MQRankSum=2.066;QD=13.29;ReadPosRankSum=0.378;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,30:71:99:972,0,1251
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|
|
1246 chr1 44214 . T C 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.627;DP=65;Dels=0.00;FS=6.471;HaplotypeScore=49.1081;MLEAC=1;MLEAF=0.500;MQ=49.76;MQ0=0;MQRankSum=-3.604;QD=0.55;ReadPosRankSum=-0.170;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,8:65:64:64,0,1916
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|
|
1247 chr1 44224 . C T 712.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.116;DP=65;Dels=0.00;FS=11.066;HaplotypeScore=41.7947;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=0;MQRankSum=3.011;QD=10.97;ReadPosRankSum=-1.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,24:65:99:741,0,1311
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|
|
1248 chr1 44226 . C T 634.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.161;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=35.0888;MLEAC=1;MLEAF=0.500;MQ=48.89;MQ0=0;MQRankSum=0.468;QD=10.58;ReadPosRankSum=1.342;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,22:60:99:663,0,1231
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|
|
1249 chr1 44227 . T C 1771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.277;DP=60;Dels=0.00;FS=3.739;HaplotypeScore=35.0888;MLEAC=1;MLEAF=0.500;MQ=48.89;MQ0=0;MQRankSum=3.270;QD=29.53;ReadPosRankSum=-1.934;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:7,52:60:43:1800,0,43
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|
|
1250 chr1 44239 . C T 1746.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=23.3747;MLEAC=2;MLEAF=1.00;MQ=50.05;MQ0=0;QD=35.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1775,138,0
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|
|
1251 chr1 44240 . C T 507.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=48;Dels=0.00;FS=2.627;HaplotypeScore=23.3747;MLEAC=1;MLEAF=0.500;MQ=50.05;MQ0=0;MQRankSum=2.800;QD=10.58;ReadPosRankSum=1.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,18:48:99:536,0,932
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|
|
1252 chr1 44241 . T C 1696.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=23.3747;MLEAC=2;MLEAF=1.00;MQ=50.05;MQ0=0;QD=27.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,47:48:99:1725,135,0
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|
|
1253 chr1 44248 . C T 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.520;DP=48;Dels=0.00;FS=9.054;HaplotypeScore=23.3746;MLEAC=1;MLEAF=0.500;MQ=50.11;MQ0=0;MQRankSum=-4.405;QD=3.08;ReadPosRankSum=2.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,10:48:99:176,0,1356
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|
|
1254 chr1 44249 . T C 178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.419;DP=49;Dels=0.00;FS=8.239;HaplotypeScore=24.3740;MLEAC=1;MLEAF=0.500;MQ=49.98;MQ0=0;MQRankSum=-4.565;QD=3.65;ReadPosRankSum=1.809;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,11:49:99:207,0,1354
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|
|
1255 chr1 44258 . T A 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.562;DP=54;Dels=0.00;FS=4.366;HaplotypeScore=24.1638;MLEAC=1;MLEAF=0.500;MQ=48.73;MQ0=0;MQRankSum=4.329;QD=10.64;ReadPosRankSum=0.018;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,19:54:99:603,0,1025
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|
|
1256 chr1 44278 . A G 1907.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=6.7023;MLEAC=2;MLEAF=1.00;MQ=46.93;MQ0=0;QD=34.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:1936,153,0
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|
|
1257 chr1 44282 . C T 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.606;DP=57;Dels=0.00;FS=1.055;HaplotypeScore=8.1141;MLEAC=1;MLEAF=0.500;MQ=45.40;MQ0=0;MQRankSum=4.194;QD=11.70;ReadPosRankSum=-1.204;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,24:57:99:695,0,881
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|
|
1258 chr1 44295 . A T 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.344;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=9.3874;MLEAC=1;MLEAF=0.500;MQ=43.43;MQ0=2;MQRankSum=-2.337;QD=0.18;ReadPosRankSum=-0.230;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,7:63:39:39,0,1747
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|
|
1259 chr1 44304 . T C 727.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.495;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=23.9832;MLEAC=1;MLEAF=0.500;MQ=43.23;MQ0=2;MQRankSum=4.033;QD=11.74;ReadPosRankSum=0.255;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,25:62:99:756,0,963
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|
|
1260 chr1 44307 . C G 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.815;DP=60;Dels=0.00;FS=6.252;HaplotypeScore=26.1832;MLEAC=1;MLEAF=0.500;MQ=43.38;MQ0=2;MQRankSum=-0.025;QD=7.33;ReadPosRankSum=-1.252;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,18:60:99:468,0,1201
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|
|
1261 chr1 44311 . A G 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.265;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=30.9134;MLEAC=1;MLEAF=0.500;MQ=43.15;MQ0=2;MQRankSum=-2.338;QD=10.90;ReadPosRankSum=-0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,29:60:99:682,0,949
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|
|
1262 chr1 44317 . T A 381.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.835;DP=59;Dels=0.00;FS=4.227;HaplotypeScore=16.7737;MLEAC=1;MLEAF=0.500;MQ=42.80;MQ0=2;MQRankSum=0.606;QD=6.47;ReadPosRankSum=-2.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,17:59:99:410,0,1154
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|
|
1263 chr1 44335 . T A 1721.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=18.1882;MLEAC=2;MLEAF=1.00;MQ=40.95;MQ0=2;QD=29.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:1750,144,0
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|
|
1264 chr1 44342 . C G 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.767;DP=61;Dels=0.00;FS=4.324;HaplotypeScore=34.0871;MLEAC=1;MLEAF=0.500;MQ=42.11;MQ0=2;MQRankSum=-1.601;QD=6.18;ReadPosRankSum=0.691;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,16:61:99:405,0,1260
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|
|
1265 chr1 44367 . C T 857.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.070;DP=57;Dels=0.00;FS=1.029;HaplotypeScore=9.9194;MLEAC=1;MLEAF=0.500;MQ=42.27;MQ0=2;MQRankSum=2.251;QD=15.05;ReadPosRankSum=0.261;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:886,0,731
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|
|
1266 chr1 44402 . T C 1512.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=18.3637;MLEAC=2;MLEAF=1.00;MQ=45.06;MQ0=0;QD=27.76;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:43:99:1541,117,0
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|
|
1267 chr1 44414 . C T 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.135;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=14.3006;MLEAC=1;MLEAF=0.500;MQ=44.91;MQ0=0;MQRankSum=0.590;QD=12.70;ReadPosRankSum=1.928;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:714,0,919
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|
|
1268 chr1 44417 . C T 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.333;DP=59;Dels=0.00;FS=7.276;HaplotypeScore=15.3006;MLEAC=1;MLEAF=0.500;MQ=45.19;MQ0=0;MQRankSum=-3.435;QD=2.13;ReadPosRankSum=-2.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,11:59:99:154,0,1624
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|
|
1269 chr1 44447 . T C 76.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.447;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=44.70;MQ0=0;MQRankSum=-0.207;QD=1.35;ReadPosRankSum=-0.960;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,7:57:99:105,0,1613
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|
|
1270 chr1 44452 . G A 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.071;DP=58;Dels=0.00;FS=3.537;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=44.96;MQ0=0;MQRankSum=-0.530;QD=2.01;ReadPosRankSum=-0.755;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,8:58:99:145,0,1592
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|
|
1271 chr1 44473 . G A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.942;DP=69;Dels=0.00;FS=9.852;HaplotypeScore=9.6363;MLEAC=1;MLEAF=0.500;MQ=44.99;MQ0=0;MQRankSum=-4.187;QD=0.71;ReadPosRankSum=0.356;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,12:69:77:77,0,2026
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|
|
1272 chr1 44477 . T C 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.028;DP=69;Dels=0.00;FS=1.548;HaplotypeScore=9.6363;MLEAC=1;MLEAF=0.500;MQ=45.04;MQ0=0;MQRankSum=-0.984;QD=1.30;ReadPosRankSum=2.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,8:69:99:118,0,1985
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|
|
1273 chr1 44478 . G C 84.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.175;DP=70;Dels=0.00;FS=1.536;HaplotypeScore=9.6363;MLEAC=1;MLEAF=0.500;MQ=45.34;MQ0=0;MQRankSum=-0.858;QD=1.21;ReadPosRankSum=2.630;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,8:70:99:113,0,2020
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|
1274 chr1 44484 . A G 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.103;DP=69;Dels=0.00;FS=1.548;HaplotypeScore=36.7273;MLEAC=1;MLEAF=0.500;MQ=45.51;MQ0=0;MQRankSum=-1.246;QD=1.13;ReadPosRankSum=2.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,8:69:99:106,0,1981
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|
|
1275 chr1 44498 . A C 296.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.439;DP=59;Dels=0.03;FS=1.285;HaplotypeScore=66.6807;MLEAC=1;MLEAF=0.500;MQ=46.25;MQ0=0;MQRankSum=1.067;QD=5.03;ReadPosRankSum=0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,12:57:99:325,0,1534
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|
|
1276 chr1 44501 . T C 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.558;DP=54;Dels=0.00;FS=2.868;HaplotypeScore=45.5620;MLEAC=1;MLEAF=0.500;MQ=45.82;MQ0=0;MQRankSum=0.142;QD=6.25;ReadPosRankSum=-0.951;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,13:54:99:366,0,1280
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|
|
1277 chr1 44503 . C T 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.095;DP=55;Dels=0.00;FS=2.476;HaplotypeScore=45.5620;MLEAC=1;MLEAF=0.500;MQ=45.92;MQ0=0;MQRankSum=-0.130;QD=18.18;ReadPosRankSum=1.776;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:1028,0,672
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|
|
1278 chr1 44505 . T C 94.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.716;DP=56;Dels=0.00;FS=1.565;HaplotypeScore=46.3941;MLEAC=1;MLEAF=0.500;MQ=46.01;MQ0=0;MQRankSum=-0.697;QD=1.69;ReadPosRankSum=-0.617;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,7:56:99:123,0,1510
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|
1279 chr1 44517 . G A 130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=8.8138;MLEAC=1;MLEAF=0.500;MQ=44.77;MQ0=0;MQRankSum=-3.350;QD=2.42;ReadPosRankSum=2.577;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,11:54:99:159,0,1479
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|
1280 chr1 44560 . G A 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.286;DP=43;Dels=0.00;FS=9.300;HaplotypeScore=4.7566;MLEAC=1;MLEAF=0.500;MQ=41.88;MQ0=0;MQRankSum=0.807;QD=9.95;ReadPosRankSum=-0.012;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,17:43:99:456,0,729
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|
|
1281 chr1 44572 . C A 1243.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.646;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=41.69;MQ0=0;MQRankSum=0.866;QD=31.09;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,39:40:99:1272,105,0
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|
|
1282 chr1 44587 . T C 345.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.665;DP=38;Dels=0.00;FS=13.265;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=40.46;MQ0=0;MQRankSum=-1.286;QD=9.10;ReadPosRankSum=-0.547;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:374,0,691
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|
|
1283 chr1 44614 . C G 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.420;DP=43;Dels=0.00;FS=1.868;HaplotypeScore=14.4733;MLEAC=1;MLEAF=0.500;MQ=42.93;MQ0=0;MQRankSum=0.020;QD=1.11;ReadPosRankSum=0.260;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,6:43:76:76,0,1119
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|
|
1284 chr1 44624 . G A 10.2 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.102;DP=51;Dels=0.00;FS=12.856;HaplotypeScore=21.4215;MLEAC=1;MLEAF=0.500;MQ=42.84;MQ0=0;MQRankSum=-2.880;QD=0.20;ReadPosRankSum=1.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,6:51:38:38,0,1509
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|
|
1285 chr1 44632 . A T 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.185;DP=54;Dels=0.00;FS=2.363;HaplotypeScore=21.5373;MLEAC=1;MLEAF=0.500;MQ=42.79;MQ0=0;MQRankSum=1.153;QD=12.81;ReadPosRankSum=-0.378;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:720,0,934
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|
|
1286 chr1 44637 . C T 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.302;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=22.5160;MLEAC=1;MLEAF=0.500;MQ=42.79;MQ0=0;MQRankSum=-0.673;QD=1.44;ReadPosRankSum=0.812;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,9:54:99:106,0,1529
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|
|
1287 chr1 44642 . C T 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.777;DP=52;Dels=0.00;FS=20.166;HaplotypeScore=24.5152;MLEAC=1;MLEAF=0.500;MQ=43.10;MQ0=0;MQRankSum=-3.351;QD=0.36;ReadPosRankSum=-0.241;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,7:52:47:47,0,1525
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|
|
1288 chr1 44646 . C T 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.224;DP=50;Dels=0.00;FS=21.581;HaplotypeScore=15.6098;MLEAC=1;MLEAF=0.500;MQ=43.77;MQ0=0;MQRankSum=-3.383;QD=0.52;ReadPosRankSum=-0.671;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,7:50:54:54,0,1474
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1289 chr1 44657 . C T 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.408;DP=58;Dels=0.00;FS=2.599;HaplotypeScore=22.8584;MLEAC=1;MLEAF=0.500;MQ=44.43;MQ0=0;MQRankSum=2.619;QD=7.03;ReadPosRankSum=0.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,15:58:99:436,0,1315
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1290 chr1 44662 . T C 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=55;Dels=0.00;FS=16.338;HaplotypeScore=20.8592;MLEAC=1;MLEAF=0.500;MQ=44.81;MQ0=0;MQRankSum=-3.253;QD=0.34;ReadPosRankSum=-0.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,6:55:47:47,0,1653
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1291 chr1 44666 . T C 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.897;DP=51;Dels=0.00;FS=4.523;HaplotypeScore=18.8632;MLEAC=1;MLEAF=0.500;MQ=45.50;MQ0=0;MQRankSum=-3.198;QD=5.00;ReadPosRankSum=0.813;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,14:51:99:283,0,1321
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1292 chr1 44682 . C T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.828;DP=48;Dels=0.00;FS=1.217;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=44.53;MQ0=0;MQRankSum=-2.438;QD=21.25;ReadPosRankSum=-0.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,34:48:99:1048,0,416
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1293 chr1 44699 . G A 1395.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=43.18;MQ0=0;QD=33.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1424,117,0
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1294 chr1 44721 . A T 442.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.754;DP=38;Dels=0.00;FS=2.913;HaplotypeScore=8.5355;MLEAC=1;MLEAF=0.500;MQ=38.46;MQ0=0;MQRankSum=1.227;QD=11.65;ReadPosRankSum=1.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:471,0,475
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1295 chr1 44722 . G A 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.575;DP=40;Dels=0.00;FS=1.222;HaplotypeScore=8.5355;MLEAC=1;MLEAF=0.500;MQ=38.48;MQ0=0;MQRankSum=0.137;QD=8.77;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,17:40:99:379,0,602
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1296 chr1 44747 . A G 853.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.64;MQ0=2;QD=23.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,36:36:75:882,75,0
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1297 chr1 44750 . T C 772.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.71;MQ0=2;QD=22.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,35:35:69:801,69,0
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1298 chr1 44764 . G A 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.890;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=31.22;MQ0=2;MQRankSum=-0.925;QD=0.33;ReadPosRankSum=0.107;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,7:42:42:42,0,799
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1299 chr1 44766 . G A 933.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.92;MQ0=2;QD=23.34;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:81:962,81,0
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1300 chr1 44844 . C T 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.998;DP=50;Dels=0.00;FS=1.117;HaplotypeScore=13.6215;MLEAC=1;MLEAF=0.500;MQ=39.32;MQ0=0;MQRankSum=0.233;QD=13.06;ReadPosRankSum=0.233;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,25:50:99:681,0,649
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1301 chr1 44846 . A G 1523.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=13.5548;MLEAC=2;MLEAF=1.00;MQ=40.00;MQ0=0;QD=32.42;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1552,123,0
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1302 chr1 44848 . G A 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.331;DP=50;Dels=0.00;FS=1.565;HaplotypeScore=12.7662;MLEAC=1;MLEAF=0.500;MQ=40.79;MQ0=0;MQRankSum=-2.924;QD=0.54;ReadPosRankSum=1.522;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:42,8:50:55:55,0,1346
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1303 chr1 44875 . C T 224.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.116;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=6.7552;MLEAC=1;MLEAF=0.500;MQ=43.15;MQ0=0;MQRankSum=-1.397;QD=3.57;ReadPosRankSum=-1.910;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:49,14:63:99:253,0,1577
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1304 chr1 44905 . C G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.316;DP=72;Dels=0.00;FS=2.379;HaplotypeScore=14.6636;MLEAC=1;MLEAF=0.500;MQ=43.09;MQ0=1;MQRankSum=0.928;QD=8.39;ReadPosRankSum=-1.284;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:49,23:72:99:632,0,1456
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1305 chr1 44912 . A G 1743.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.677;DP=68;Dels=0.00;FS=1.336;HaplotypeScore=30.8580;MLEAC=1;MLEAF=0.500;MQ=43.96;MQ0=2;MQRankSum=-0.403;QD=25.64;ReadPosRankSum=-1.903;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:15,53:68:99:1772,0,267
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1306 chr1 44920 . T C 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.714;DP=73;Dels=0.00;FS=7.931;HaplotypeScore=5.9984;MLEAC=1;MLEAF=0.500;MQ=42.33;MQ0=4;MQRankSum=-0.128;QD=5.48;ReadPosRankSum=1.793;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:52,21:73:99:428,0,1524
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1307 chr1 44950 . T C 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=4.8653;MLEAC=1;MLEAF=0.500;MQ=38.40;MQ0=5;MQRankSum=0.127;QD=7.52;ReadPosRankSum=1.502;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:48,23:72:99:570,0,1227
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1308 chr1 44968 . A G 1512.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=4.8653;MLEAC=2;MLEAF=1.00;MQ=35.93;MQ0=5;QD=25.21;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,60:60:99:1541,132,0
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1309 chr1 44980 . T G 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.482;DP=53;Dels=0.00;FS=1.794;HaplotypeScore=4.8653;MLEAC=1;MLEAF=0.500;MQ=32.25;MQ0=6;MQRankSum=0.207;QD=17.41;ReadPosRankSum=-1.100;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,47:53:53:951,0,53
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1310 chr1 44999 . A G 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.117;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=8.8333;MLEAC=1;MLEAF=0.500;MQ=30.81;MQ0=6;MQRankSum=-2.111;QD=4.22;ReadPosRankSum=-0.168;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,22:48:99:231,0,671
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1311 chr1 45005 . G A 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.014;DP=44;Dels=0.00;FS=5.608;HaplotypeScore=21.5580;MLEAC=1;MLEAF=0.500;MQ=30.42;MQ0=4;MQRankSum=1.637;QD=10.11;ReadPosRankSum=1.096;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,20:44:99:473,0,341
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1312 chr1 45011 . A G 805.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=15.6852;MLEAC=2;MLEAF=1.00;MQ=30.05;MQ0=2;QD=21.20;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,37:38:78:834,78,0
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1313 chr1 45027 . C T 849.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=1.9559;MLEAC=2;MLEAF=1.00;MQ=31.41;MQ0=4;QD=20.23;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,42:42:78:878,78,0
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1314 chr1 45055 . C T 66.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.634;DP=71;Dels=0.00;FS=12.767;HaplotypeScore=11.6629;MLEAC=1;MLEAF=0.500;MQ=43.94;MQ0=9;MQRankSum=-0.438;QD=0.94;ReadPosRankSum=-0.182;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:53,15:71:95:95,0,1604
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1315 chr1 45090 . C T 1075.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.677;DP=87;Dels=0.00;FS=4.246;HaplotypeScore=45.0201;MLEAC=1;MLEAF=0.500;MQ=49.72;MQ0=1;MQRankSum=3.081;QD=12.37;ReadPosRankSum=-0.758;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:52,34:87:99:1104,0,1445
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1316 chr1 45092 . C T 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.793;DP=86;Dels=0.00;FS=18.933;HaplotypeScore=45.0201;MLEAC=1;MLEAF=0.500;MQ=49.98;MQ0=1;MQRankSum=-0.050;QD=0.57;ReadPosRankSum=-0.221;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:77,9:86:77:77,0,2524
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1317 chr1 45093 . A C 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.723;DP=84;Dels=0.04;FS=4.282;HaplotypeScore=44.0211;MLEAC=1;MLEAF=0.500;MQ=50.41;MQ0=1;MQRankSum=-2.754;QD=0.47;ReadPosRankSum=0.306;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:64,16:81:68:68,0,2273
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1318 chr1 45100 . A T 1063.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.790;DP=91;Dels=0.00;FS=1.785;HaplotypeScore=46.2820;MLEAC=1;MLEAF=0.500;MQ=50.63;MQ0=1;MQRankSum=0.114;QD=11.69;ReadPosRankSum=1.119;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:57,34:91:99:1092,0,1575
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1319 chr1 45104 . C T 1245.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.511;DP=93;Dels=0.00;FS=5.290;HaplotypeScore=20.4240;MLEAC=1;MLEAF=0.500;MQ=51.13;MQ0=1;MQRankSum=1.122;QD=13.40;ReadPosRankSum=-0.845;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:55,38:93:99:1274,0,1627
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1320 chr1 45135 . C T 1475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.219;DP=93;Dels=0.00;FS=0.788;HaplotypeScore=3.1233;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=0.496;QD=15.87;ReadPosRankSum=-0.019;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,46:93:99:1504,0,1552
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1321 chr1 45155 . C T 3133.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.690;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=145.5703;MLEAC=2;MLEAF=1.00;MQ=50.31;MQ0=0;MQRankSum=1.436;QD=30.69;ReadPosRankSum=-0.338;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,81:82:99:3162,241,0
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1322 chr1 45200 . A T 2113.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=47.61;MQ0=1;QD=32.38;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2142,169,0
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1323 chr1 45254 . G A 2049.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=47.40;MQ0=0;QD=29.96;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2078,156,0
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1324 chr1 45271 . C T 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.331;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=3.1435;MLEAC=1;MLEAF=0.500;MQ=48.86;MQ0=0;MQRankSum=0.761;QD=14.36;ReadPosRankSum=-0.072;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,26:58:99:861,0,1025
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1325 chr1 45272 . C A 2207.77 . AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=3.1435;MLEAC=2;MLEAF=1.00;MQ=48.86;MQ0=0;QD=33.93;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,58:58:99:2236,169,0
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1326 chr1 45286 . G A 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=1.7329;MLEAC=1;MLEAF=0.500;MQ=49.43;MQ0=0;MQRankSum=0.497;QD=16.06;ReadPosRankSum=0.752;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,31:64:99:1056,0,1087
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1327 chr1 45290 . T A 1146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.598;DP=65;Dels=0.00;FS=2.073;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=49.75;MQ0=0;MQRankSum=-0.151;QD=17.64;ReadPosRankSum=0.190;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,34:65:99:1175,0,1019
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1328 chr1 45343 . T A 1246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.611;DP=74;Dels=0.00;FS=3.119;HaplotypeScore=3.9919;MLEAC=1;MLEAF=0.500;MQ=51.54;MQ0=0;MQRankSum=1.189;QD=16.85;ReadPosRankSum=0.605;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:37,37:74:99:1275,0,1131
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1329 chr1 45344 . G A 2859.77 . AC=2;AF=1.00;AN=2;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=2.9920;MLEAC=2;MLEAF=1.00;MQ=51.54;MQ0=0;QD=33.68;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,74:74:99:2888,220,0
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1330 chr1 45355 . T C 2778.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.98;MQ0=0;QD=24.35;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,72:72:99:2807,211,0
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1331 chr1 45366 . A C 2847.77 . AC=2;AF=1.00;AN=2;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.43;MQ0=0;QD=31.96;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,75:75:99:2876,220,0
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1332 chr1 45377 . C T 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.613;DP=72;Dels=0.00;FS=27.679;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.59;MQ0=0;MQRankSum=-2.895;QD=0.71;ReadPosRankSum=-1.328;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:63,9:72:79:79,0,2293
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1333 chr1 45382 . A G 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.364;DP=74;Dels=0.00;FS=24.375;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.91;MQ0=0;MQRankSum=-3.126;QD=0.20;ReadPosRankSum=0.050;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:65,9:74:43:43,0,2344
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1334 chr1 45385 . T A 2874.77 . AC=2;AF=1.00;AN=2;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=2;MLEAF=1.00;MQ=50.94;MQ0=0;QD=27.46;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,75:75:99:2903,220,0
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1335 chr1 45401 . T G 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.147;DP=75;Dels=0.00;FS=42.438;HaplotypeScore=1.8656;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=0;MQRankSum=-2.624;QD=2.74;ReadPosRankSum=2.484;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,13:75:99:234,0,2260
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1336 chr1 45425 . T C 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.597;DP=62;Dels=0.00;FS=32.888;HaplotypeScore=11.8192;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=-3.715;QD=3.33;ReadPosRankSum=2.040;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:50,12:62:99:235,0,1811
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1337 chr1 45428 . C A 2117.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=21.6418;MLEAC=2;MLEAF=1.00;MQ=53.19;MQ0=0;QD=27.70;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2146,163,0
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1338 chr1 45430 . C A 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.713;DP=50;Dels=0.00;FS=4.121;HaplotypeScore=21.6418;MLEAC=1;MLEAF=0.500;MQ=53.45;MQ0=0;MQRankSum=0.980;QD=12.74;ReadPosRankSum=0.446;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:30,20:50:99:665,0,987
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1339 chr1 45435 . T C 1851.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=30.4494;MLEAC=2;MLEAF=1.00;MQ=54.04;MQ0=0;QD=26.85;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1880,141,0
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1340 chr1 45436 . C T 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.196;DP=48;Dels=0.00;FS=17.629;HaplotypeScore=19.6275;MLEAC=1;MLEAF=0.500;MQ=54.52;MQ0=0;MQRankSum=-3.668;QD=3.45;ReadPosRankSum=0.470;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:38,10:48:99:194,0,1412
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1341 chr1 45442 . G A 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.766;DP=53;Dels=0.00;FS=20.851;HaplotypeScore=20.6274;MLEAC=1;MLEAF=0.500;MQ=53.74;MQ0=0;MQRankSum=-3.761;QD=3.49;ReadPosRankSum=-0.055;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:42,11:53:99:213,0,1458
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1342 chr1 45445 . G A 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.117;DP=54;Dels=0.00;FS=3.890;HaplotypeScore=20.6274;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=0;MQRankSum=0.857;QD=15.44;ReadPosRankSum=-0.441;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,26:54:99:862,0,877
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1343 chr1 45455 . C T 1668.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=21.9167;MLEAC=2;MLEAF=1.00;MQ=54.86;MQ0=0;QD=33.46;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1697,132,0
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1344 chr1 45456 . A G 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.281;DP=47;Dels=0.00;FS=15.317;HaplotypeScore=22.9164;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=0;MQRankSum=-2.324;QD=20.91;ReadPosRankSum=-1.560;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,31:47:99:1011,0,399
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1345 chr1 45458 . C A 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.943;DP=49;Dels=0.00;FS=1.157;HaplotypeScore=24.9247;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=0.389;QD=9.83;ReadPosRankSum=0.305;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,17:49:99:510,0,1061
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1346 chr1 45460 . C T 101.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.945;DP=51;Dels=0.00;FS=20.268;HaplotypeScore=33.8333;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=-2.966;QD=2.00;ReadPosRankSum=-0.712;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,8:51:99:130,0,1482
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1347 chr1 45468 . T C 489.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.974;DP=54;Dels=0.00;FS=11.572;HaplotypeScore=42.6787;MLEAC=1;MLEAF=0.500;MQ=54.16;MQ0=0;MQRankSum=3.688;QD=9.07;ReadPosRankSum=0.354;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:37,17:54:99:518,0,1120
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1348 chr1 45469 . C G 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.692;DP=54;Dels=0.00;FS=25.872;HaplotypeScore=26.8594;MLEAC=1;MLEAF=0.500;MQ=54.16;MQ0=0;MQRankSum=-2.910;QD=1.38;ReadPosRankSum=-0.791;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:46,8:54:99:103,0,1615
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1349 chr1 45473 . G A 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.252;DP=57;Dels=0.00;FS=27.090;HaplotypeScore=18.7370;MLEAC=1;MLEAF=0.500;MQ=53.42;MQ0=0;MQRankSum=-3.140;QD=1.47;ReadPosRankSum=-0.864;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:48,9:57:99:112,0,1689
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1350 chr1 45486 . T G 42.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=59;Dels=0.00;FS=26.386;HaplotypeScore=19.2723;MLEAC=1;MLEAF=0.500;MQ=52.31;MQ0=0;MQRankSum=-3.044;QD=0.72;ReadPosRankSum=-0.122;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:51,8:59:71:71,0,1772
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1351 chr1 45491 . T C 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.621;DP=56;Dels=0.00;FS=11.681;HaplotypeScore=17.2627;MLEAC=1;MLEAF=0.500;MQ=51.49;MQ0=0;MQRankSum=2.678;QD=7.98;ReadPosRankSum=-0.991;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:39,16:56:99:475,0,1141
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1352 chr1 45492 . A C 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.556;DP=56;Dels=0.00;FS=36.390;HaplotypeScore=17.2627;MLEAC=1;MLEAF=0.500;MQ=51.49;MQ0=0;MQRankSum=-3.873;QD=1.34;ReadPosRankSum=-0.513;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:46,10:56:99:103,0,1545
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1353 chr1 45515 . A C 249.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.473;DP=55;Dels=0.00;FS=18.588;HaplotypeScore=36.5629;MLEAC=1;MLEAF=0.500;MQ=47.91;MQ0=0;MQRankSum=1.483;QD=4.54;ReadPosRankSum=1.105;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:44,11:55:99:278,0,1358
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1354 chr1 45516 . T C 103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=55;Dels=0.00;FS=32.991;HaplotypeScore=36.5629;MLEAC=1;MLEAF=0.500;MQ=47.72;MQ0=0;MQRankSum=-5.064;QD=1.89;ReadPosRankSum=0.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,12:55:99:132,0,1550
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1355 chr1 45518 . C T 130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.102;DP=57;Dels=0.00;FS=26.291;HaplotypeScore=37.5622;MLEAC=1;MLEAF=0.500;MQ=47.75;MQ0=0;MQRankSum=-5.240;QD=2.29;ReadPosRankSum=-0.162;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:44,13:57:99:159,0,1581
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1356 chr1 45530 . G A 1057.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.884;DP=61;Dels=0.00;FS=1.071;HaplotypeScore=2.8319;MLEAC=1;MLEAF=0.500;MQ=46.23;MQ0=1;MQRankSum=4.182;QD=17.34;ReadPosRankSum=-0.133;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,32:61:99:1086,0,615
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1357 chr1 45538 . T C 2219.77 . AC=2;AF=1.00;AN=2;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=2.8319;MLEAC=2;MLEAF=1.00;MQ=45.96;MQ0=1;QD=33.13;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,67:67:99:2248,175,0
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1358 chr1 45549 . G A 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.457;DP=67;Dels=0.00;FS=21.346;HaplotypeScore=8.9982;MLEAC=1;MLEAF=0.500;MQ=45.62;MQ0=1;MQRankSum=1.140;QD=2.58;ReadPosRankSum=0.504;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:58,9:67:99:201,0,1627
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1359 chr1 45550 . A G 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.636;DP=67;Dels=0.00;FS=0.940;HaplotypeScore=8.9982;MLEAC=1;MLEAF=0.500;MQ=46.27;MQ0=1;MQRankSum=-4.933;QD=9.31;ReadPosRankSum=0.982;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,33:67:99:652,0,1160
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1360 chr1 45576 . A T 455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.949;DP=86;Dels=0.00;FS=0.996;HaplotypeScore=31.9081;MLEAC=1;MLEAF=0.500;MQ=44.67;MQ0=1;MQRankSum=-3.062;QD=5.30;ReadPosRankSum=0.000;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:60,26:86:99:484,0,1787
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1361 chr1 45578 . A G 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.189;DP=84;Dels=0.00;FS=6.011;HaplotypeScore=57.3640;MLEAC=1;MLEAF=0.500;MQ=44.80;MQ0=1;MQRankSum=-6.448;QD=10.99;ReadPosRankSum=-1.326;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:40,44:84:99:951,0,1314
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1362 chr1 45586 . T C 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.575;DP=80;Dels=0.00;FS=1.341;HaplotypeScore=88.2105;MLEAC=1;MLEAF=0.500;MQ=45.39;MQ0=1;MQRankSum=-4.105;QD=0.92;ReadPosRankSum=-0.165;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:66,14:80:99:102,0,2084
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1363 chr1 45587 . G A 95.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.469;DP=80;Dels=0.00;FS=1.232;HaplotypeScore=75.5755;MLEAC=1;MLEAF=0.500;MQ=45.39;MQ0=1;MQRankSum=-4.092;QD=1.20;ReadPosRankSum=-0.086;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:66,14:80:99:124,0,2088
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1364 chr1 45588 . A G 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=81;Dels=0.00;FS=1.248;HaplotypeScore=76.3642;MLEAC=1;MLEAF=0.500;MQ=45.60;MQ0=1;MQRankSum=-4.082;QD=1.15;ReadPosRankSum=0.026;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:67,14:81:99:121,0,2109
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1365 chr1 45600 . G A 1328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=109;Dels=0.00;FS=1.699;HaplotypeScore=36.6790;MLEAC=1;MLEAF=0.500;MQ=42.25;MQ0=2;MQRankSum=-6.013;QD=12.19;ReadPosRankSum=0.815;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:46,63:109:99:1357,0,1334
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1366 chr1 45609 . A C 746.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.395;DP=114;Dels=0.00;FS=0.838;HaplotypeScore=28.9230;MLEAC=1;MLEAF=0.500;MQ=42.08;MQ0=2;MQRankSum=-1.161;QD=6.55;ReadPosRankSum=1.490;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,34:114:99:775,0,2078
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1367 chr1 45619 . C T 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=119;Dels=0.00;FS=2.580;HaplotypeScore=3.6750;MLEAC=1;MLEAF=0.500;MQ=40.98;MQ0=2;MQRankSum=-0.216;QD=7.02;ReadPosRankSum=1.214;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:83,36:119:99:864,0,1946
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1368 chr1 45632 . G T 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.393;DP=119;Dels=0.00;FS=0.893;HaplotypeScore=6.6304;MLEAC=1;MLEAF=0.500;MQ=40.17;MQ0=2;MQRankSum=-5.708;QD=2.94;ReadPosRankSum=1.745;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:82,37:119:99:378,0,2346
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1369 chr1 45659 . C T 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.317;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=71.6402;MLEAC=1;MLEAF=0.500;MQ=41.20;MQ0=3;MQRankSum=-6.632;QD=3.24;ReadPosRankSum=0.893;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,39:120:99:417,0,2397
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1370 chr1 45660 . A G 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.966;DP=117;Dels=0.00;FS=2.575;HaplotypeScore=63.3294;MLEAC=1;MLEAF=0.500;MQ=41.50;MQ0=3;MQRankSum=-1.543;QD=0.31;ReadPosRankSum=1.048;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:102,14:117:64:64,0,2593
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1371 chr1 45663 . C T 27.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.724;DP=116;Dels=0.00;FS=2.578;HaplotypeScore=119.3449;MLEAC=1;MLEAF=0.500;MQ=41.26;MQ0=3;MQRankSum=-1.489;QD=0.24;ReadPosRankSum=1.354;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:102,14:116:56:56,0,2716
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1372 chr1 45672 . T G 886.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.828;DP=105;Dels=0.00;FS=0.751;HaplotypeScore=110.4878;MLEAC=1;MLEAF=0.500;MQ=43.52;MQ0=2;MQRankSum=-5.196;QD=8.45;ReadPosRankSum=0.761;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:60,45:105:99:915,0,1759
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1373 chr1 45673 . G A 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.793;DP=105;Dels=0.00;FS=0.897;HaplotypeScore=111.2217;MLEAC=1;MLEAF=0.500;MQ=43.63;MQ0=2;MQRankSum=-5.747;QD=1.35;ReadPosRankSum=1.937;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,24:105:99:170,0,2516
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1374 chr1 45679 . C T 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.082;DP=116;Dels=0.00;FS=2.067;HaplotypeScore=85.5662;MLEAC=1;MLEAF=0.500;MQ=43.87;MQ0=2;MQRankSum=-0.621;QD=3.21;ReadPosRankSum=-0.794;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,23:116:99:401,0,2219
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1375 chr1 45694 . A G 217.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.354;DP=125;Dels=0.00;FS=4.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.00;MQ0=2;MQRankSum=-5.132;QD=1.74;ReadPosRankSum=-0.229;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:100,25:125:99:246,0,3244
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1376 chr1 45707 . T C 2311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.424;DP=121;Dels=0.00;FS=6.874;HaplotypeScore=39.0259;MLEAC=1;MLEAF=0.500;MQ=45.33;MQ0=2;MQRankSum=-7.286;QD=19.11;ReadPosRankSum=0.335;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,87:121:99:2340,0,940
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1377 chr1 45717 . G A 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.975;DP=109;Dels=0.00;FS=1.591;HaplotypeScore=73.3895;MLEAC=1;MLEAF=0.500;MQ=45.70;MQ0=2;MQRankSum=-1.982;QD=6.89;ReadPosRankSum=2.664;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:65,43:109:99:779,0,1809
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1378 chr1 45724 . C G 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.854;DP=100;Dels=0.00;FS=0.957;HaplotypeScore=83.7585;MLEAC=1;MLEAF=0.500;MQ=46.80;MQ0=2;MQRankSum=-1.008;QD=5.78;ReadPosRankSum=1.509;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,25:100:99:606,0,1819
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1379 chr1 45725 . C T 426.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.812;DP=98;Dels=0.00;FS=0.966;HaplotypeScore=96.3231;MLEAC=1;MLEAF=0.500;MQ=46.88;MQ0=2;MQRankSum=5.039;QD=4.35;ReadPosRankSum=-2.841;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:79,19:98:99:455,0,2414
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1380 chr1 45727 . A G 3406.77 . AC=2;AF=1.00;AN=2;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=131.4140;MLEAC=2;MLEAF=1.00;MQ=46.96;MQ0=2;QD=34.41;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,99:99:99:3435,274,0
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1381 chr1 45728 . T C 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.069;DP=100;Dels=0.00;FS=12.270;HaplotypeScore=130.4542;MLEAC=1;MLEAF=0.500;MQ=46.88;MQ0=2;MQRankSum=-0.733;QD=1.80;ReadPosRankSum=3.540;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:87,13:100:99:208,0,2628
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1382 chr1 45729 . A G 933.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.199;DP=98;Dels=0.00;FS=7.239;HaplotypeScore=143.0188;MLEAC=1;MLEAF=0.500;MQ=47.26;MQ0=2;MQRankSum=-2.286;QD=9.53;ReadPosRankSum=1.533;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,35:98:99:962,0,1812
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1383 chr1 45733 . C T 212.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.767;DP=103;Dels=0.00;FS=11.158;HaplotypeScore=175.1243;MLEAC=1;MLEAF=0.500;MQ=45.48;MQ0=2;MQRankSum=-0.096;QD=2.07;ReadPosRankSum=2.500;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:90,13:103:99:241,0,2768
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1384 chr1 45744 . A T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.996;DP=97;Dels=0.00;FS=3.403;HaplotypeScore=141.3914;MLEAC=1;MLEAF=0.500;MQ=43.52;MQ0=6;MQRankSum=-2.164;QD=0.15;ReadPosRankSum=0.983;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:86,11:97:43:43,0,2548
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1385 chr1 45746 . C G 1081.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.871;DP=98;Dels=0.00;FS=5.658;HaplotypeScore=144.7874;MLEAC=1;MLEAF=0.500;MQ=43.28;MQ0=6;MQRankSum=-2.422;QD=11.04;ReadPosRankSum=-1.217;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:57,41:98:99:1110,0,1505
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1386 chr1 45749 . G A 60.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.332;DP=105;Dels=0.00;FS=20.438;HaplotypeScore=99.1311;MLEAC=1;MLEAF=0.500;MQ=42.61;MQ0=6;MQRankSum=-1.228;QD=0.58;ReadPosRankSum=1.410;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:93,12:105:89:89,0,2686
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1387 chr1 45752 . C A 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.973;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=60.4379;MLEAC=1;MLEAF=0.500;MQ=42.32;MQ0=7;MQRankSum=3.784;QD=2.22;ReadPosRankSum=3.512;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:91,16:107:99:266,0,2493
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1388 chr1 45756 . T C 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.279;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=54.1966;MLEAC=1;MLEAF=0.500;MQ=41.83;MQ0=7;MQRankSum=3.711;QD=3.90;ReadPosRankSum=2.139;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:86,19:105:99:438,0,2316
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1389 chr1 45774 . G A 2856.77 . AC=2;AF=1.00;AN=2;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=1.8661;MLEAC=2;MLEAF=1.00;MQ=40.57;MQ0=8;QD=29.15;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,98:98:99:2885,247,0
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1390 chr1 45792 . A T 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.132;DP=73;Dels=0.00;FS=9.059;HaplotypeScore=58.8320;MLEAC=1;MLEAF=0.500;MQ=32.74;MQ0=7;MQRankSum=-2.340;QD=8.15;ReadPosRankSum=-0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,26:73:99:623,0,946
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1391 chr1 45793 . A T 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.182;DP=74;Dels=0.00;FS=6.479;HaplotypeScore=58.8320;MLEAC=1;MLEAF=0.500;MQ=32.71;MQ0=7;MQRankSum=-1.025;QD=10.97;ReadPosRankSum=-1.339;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:42,32:74:99:840,0,770
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1392 chr1 45796 . T A 173.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.474;DP=73;Dels=0.03;FS=11.097;HaplotypeScore=57.0004;MLEAC=1;MLEAF=0.500;MQ=32.88;MQ0=7;MQRankSum=-0.761;QD=2.38;ReadPosRankSum=3.011;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:55,16:71:99:202,0,1418
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1393 chr1 45803 . C T 2095.77 . AC=2;AF=1.00;AN=2;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=66.1329;MLEAC=2;MLEAF=1.00;MQ=33.59;MQ0=6;QD=27.58;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,76:76:99:2124,183,0
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1394 chr1 45826 . A T 1113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.844;DP=78;Dels=0.01;FS=3.363;HaplotypeScore=5.1586;MLEAC=1;MLEAF=0.500;MQ=36.05;MQ0=3;MQRankSum=-3.121;QD=14.28;ReadPosRankSum=2.318;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,46:77:99:1142,0,798
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1395 chr1 45844 . T A 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.235;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=38.54;MQ0=3;MQRankSum=-3.089;QD=4.97;ReadPosRankSum=0.299;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:71,25:96:99:505,0,2123
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1396 chr1 45863 . A T 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.601;DP=97;Dels=0.00;FS=0.931;HaplotypeScore=2.8214;MLEAC=1;MLEAF=0.500;MQ=39.70;MQ0=1;MQRankSum=3.322;QD=5.27;ReadPosRankSum=-0.737;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:72,22:97:99:539,0,2180
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1397 chr1 45895 . C T 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.467;DP=86;Dels=0.00;FS=3.221;HaplotypeScore=19.6124;MLEAC=1;MLEAF=0.500;MQ=40.11;MQ0=2;MQRankSum=2.945;QD=7.57;ReadPosRankSum=1.653;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:61,25:86:99:679,0,1779
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1398 chr1 45899 . T G 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.443;DP=84;Dels=0.00;FS=5.870;HaplotypeScore=19.6124;MLEAC=1;MLEAF=0.500;MQ=39.85;MQ0=3;MQRankSum=-2.045;QD=4.13;ReadPosRankSum=-0.184;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:64,20:84:99:375,0,1957
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1399 chr1 45911 . C T 1407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.206;DP=77;Dels=0.00;FS=0.933;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=39.22;MQ0=3;MQRankSum=-3.291;QD=18.28;ReadPosRankSum=1.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,51:77:99:1436,0,660
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1400 chr1 45928 . G A 241.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.364;DP=63;Dels=0.00;FS=1.202;HaplotypeScore=13.5950;MLEAC=1;MLEAF=0.500;MQ=38.77;MQ0=3;MQRankSum=-2.063;QD=3.84;ReadPosRankSum=-0.054;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:50,13:63:99:270,0,1333
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1401 chr1 45929 . C G 213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.620;DP=63;Dels=0.00;FS=1.173;HaplotypeScore=13.5950;MLEAC=1;MLEAF=0.500;MQ=38.77;MQ0=3;MQRankSum=-1.844;QD=3.39;ReadPosRankSum=0.603;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:48,15:63:99:242,0,1410
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1402 chr1 45934 . T C 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.163;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=10.8117;MLEAC=1;MLEAF=0.500;MQ=38.27;MQ0=3;MQRankSum=-1.596;QD=3.36;ReadPosRankSum=0.489;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:41,14:55:99:213,0,1231
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1403 chr1 45957 . T C 80.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155;DP=26;Dels=0.00;FS=2.754;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=32.58;MQ0=3;MQRankSum=-0.385;QD=3.11;ReadPosRankSum=0.385;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,7:26:99:109,0,455
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1404 chr1 45965 . T C 275.78 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.61;MQ0=2;QD=19.70;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,14:14:27:304,27,0
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1405 chr1 45991 . T C 138.9 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.85;MQ0=1;QD=19.84;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,7:7:15:167,15,0
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1406 chr1 46015 . T A 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.081;DP=29;Dels=0.00;FS=2.093;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=30.27;MQ0=6;MQRankSum=-1.304;QD=1.89;ReadPosRankSum=0.559;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,5:29:83:83,0,581
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1407 chr1 46016 . G T 56.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.155;DP=29;Dels=0.00;FS=2.093;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=30.27;MQ0=6;MQRankSum=-1.304;QD=1.96;ReadPosRankSum=0.559;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,5:29:85:85,0,588
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1408 chr1 46017 . A G 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=2.239;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=30.40;MQ0=7;MQRankSum=-1.457;QD=0.72;ReadPosRankSum=1.386;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,4:33:52:52,0,712
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1409 chr1 46033 . A C 128.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.857;DP=62;Dels=0.00;FS=17.444;HaplotypeScore=12.6635;MLEAC=1;MLEAF=0.500;MQ=30.48;MQ0=9;MQRankSum=0.683;QD=2.08;ReadPosRankSum=0.683;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:54,8:62:99:157,0,1251
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1410 chr1 46036 . C T 1669.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=12.6635;MLEAC=2;MLEAF=1.00;MQ=29.79;MQ0=10;QD=25.69;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,65:65:99:1698,141,0
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1411 chr1 46051 . G A 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;DP=90;Dels=0.00;FS=6.369;HaplotypeScore=23.7978;MLEAC=1;MLEAF=0.500;MQ=30.89;MQ0=10;MQRankSum=-1.053;QD=5.56;ReadPosRankSum=1.556;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:64,26:90:99:529,0,1416
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1412 chr1 46062 . T A 1644.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.702;DP=97;Dels=0.00;FS=0.875;HaplotypeScore=24.1654;MLEAC=1;MLEAF=0.500;MQ=31.34;MQ0=10;MQRankSum=2.289;QD=16.96;ReadPosRankSum=2.106;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:35,62:97:99:1673,0,454
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1413 chr1 46064 . T C 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.201;DP=99;Dels=0.00;FS=7.151;HaplotypeScore=24.1654;MLEAC=1;MLEAF=0.500;MQ=31.03;MQ0=10;MQRankSum=-1.046;QD=0.26;ReadPosRankSum=-0.955;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:87,12:99:54:54,0,2051
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1414 chr1 46073 . A T 1710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=111;Dels=0.00;FS=0.000;HaplotypeScore=18.4418;MLEAC=1;MLEAF=0.500;MQ=30.65;MQ0=10;MQRankSum=3.059;QD=15.41;ReadPosRankSum=3.428;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,64:111:99:1739,0,618
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1415 chr1 46082 . C T 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.677;DP=119;Dels=0.00;FS=2.762;HaplotypeScore=10.8856;MLEAC=1;MLEAF=0.500;MQ=30.51;MQ0=11;MQRankSum=-0.591;QD=0.29;ReadPosRankSum=1.598;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:105,14:119:63:63,0,2389
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1416 chr1 46123 . T A 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.952;DP=118;Dels=0.00;FS=2.620;HaplotypeScore=14.0204;MLEAC=1;MLEAF=0.500;MQ=29.74;MQ0=16;MQRankSum=0.492;QD=1.49;ReadPosRankSum=-1.118;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:99,19:118:99:204,0,2132
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1417 chr1 46130 . G C 1124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.815;DP=113;Dels=0.00;FS=0.000;HaplotypeScore=12.9254;MLEAC=1;MLEAF=0.500;MQ=28.94;MQ0=18;MQRankSum=2.438;QD=9.95;ReadPosRankSum=0.465;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:59,54:113:99:1153,0,946
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1418 chr1 46134 . A C 1117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.083;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=28.45;MQ0=19;MQRankSum=3.071;QD=10.54;ReadPosRankSum=0.327;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:54,52:106:99:1146,0,745
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1419 chr1 46151 . A C 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.894;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=29.0289;MLEAC=1;MLEAF=0.500;MQ=26.70;MQ0=23;MQRankSum=2.003;QD=2.89;ReadPosRankSum=2.356;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,22:96:99:306,0,1339
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1420 chr1 46158 . G C 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.411;DP=96;Dels=0.00;FS=1.341;HaplotypeScore=39.0149;MLEAC=1;MLEAF=0.500;MQ=26.29;MQ0=24;MQRankSum=1.288;QD=2.65;ReadPosRankSum=2.514;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:71,22:96:99:283,0,1187
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1421 chr1 46169 . C A 162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.488;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=33.7549;MLEAC=1;MLEAF=0.500;MQ=29.68;MQ0=25;MQRankSum=0.853;QD=1.55;ReadPosRankSum=-0.449;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:89,14:105:99:191,0,1752
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1422 chr1 46178 . A G 543.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.132;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=40.5352;MLEAC=1;MLEAF=0.500;MQ=29.80;MQ0=26;MQRankSum=1.065;QD=5.13;ReadPosRankSum=-0.715;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:72,32:106:99:572,0,1382
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1423 chr1 46199 . T G 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.172;DP=90;Dels=0.00;FS=0.000;HaplotypeScore=146.8097;MLEAC=1;MLEAF=0.500;MQ=35.49;MQ0=8;MQRankSum=0.538;QD=3.53;ReadPosRankSum=-0.275;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:73,17:90:99:346,0,1892
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1424 chr1 46203 . T C 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.356;DP=95;Dels=0.00;FS=4.713;HaplotypeScore=115.8313;MLEAC=1;MLEAF=0.500;MQ=36.73;MQ0=7;MQRankSum=2.951;QD=8.13;ReadPosRankSum=-0.685;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:63,30:95:99:801,0,1544
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1425 chr1 46204 . A G 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.027;DP=99;Dels=0.00;FS=1.263;HaplotypeScore=104.3565;MLEAC=1;MLEAF=0.500;MQ=36.99;MQ0=7;MQRankSum=-3.158;QD=1.27;ReadPosRankSum=2.038;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:85,14:99:99:154,0,2379
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1426 chr1 46209 . G C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.064;DP=105;Dels=0.00;FS=2.148;HaplotypeScore=73.4158;MLEAC=1;MLEAF=0.500;MQ=37.74;MQ0=6;MQRankSum=-0.435;QD=4.08;ReadPosRankSum=1.073;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,22:105:99:457,0,2172
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1427 chr1 46217 . A T 843.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.595;DP=107;Dels=0.00;FS=7.349;HaplotypeScore=36.8004;MLEAC=1;MLEAF=0.500;MQ=38.39;MQ0=6;MQRankSum=2.982;QD=7.89;ReadPosRankSum=-0.040;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,33:107:99:872,0,1991
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1428 chr1 46223 . A T 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.004;DP=110;Dels=0.00;FS=16.066;HaplotypeScore=84.6532;MLEAC=1;MLEAF=0.500;MQ=39.41;MQ0=4;MQRankSum=3.566;QD=7.08;ReadPosRankSum=0.579;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,30:110:99:807,0,2258
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1429 chr1 46259 . A C 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.583;DP=125;Dels=0.00;FS=8.544;HaplotypeScore=18.7174;MLEAC=1;MLEAF=0.500;MQ=39.29;MQ0=5;MQRankSum=-2.002;QD=5.90;ReadPosRankSum=0.318;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:68,35:125:99:766,0,2032
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1430 chr1 46279 . G T 1314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.148;DP=126;Dels=0.00;FS=16.583;HaplotypeScore=16.7188;MLEAC=1;MLEAF=0.500;MQ=36.95;MQ0=11;MQRankSum=-2.173;QD=10.43;ReadPosRankSum=1.178;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,64:126:99:1343,0,1687
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1431 chr1 46288 . A T 268.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.151;DP=124;Dels=0.00;FS=0.000;HaplotypeScore=25.9225;MLEAC=1;MLEAF=0.500;MQ=35.56;MQ0=13;MQRankSum=-0.037;QD=2.17;ReadPosRankSum=0.340;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:103,21:124:99:297,0,2552
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1432 chr1 46293 . T A 3320.77 . AC=2;AF=1.00;AN=2;DP=124;Dels=0.00;FS=0.000;HaplotypeScore=27.7337;MLEAC=2;MLEAF=1.00;MQ=34.88;MQ0=13;QD=26.78;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,124:124:99:3349,268,0
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1433 chr1 46297 . C T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.498;DP=123;Dels=0.00;FS=1.177;HaplotypeScore=28.4676;MLEAC=1;MLEAF=0.500;MQ=34.77;MQ0=13;MQRankSum=-1.404;QD=1.19;ReadPosRankSum=0.112;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:108,15:123:99:174,0,2572
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1434 chr1 46303 . T C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=113;Dels=0.00;FS=5.395;HaplotypeScore=31.8222;MLEAC=1;MLEAF=0.500;MQ=33.25;MQ0=13;MQRankSum=-0.279;QD=4.00;ReadPosRankSum=0.573;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:82,31:113:99:480,0,1952
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1435 chr1 46311 . T C 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.501;DP=106;Dels=0.00;FS=4.629;HaplotypeScore=71.9889;MLEAC=1;MLEAF=0.500;MQ=31.67;MQ0=13;MQRankSum=-1.015;QD=2.43;ReadPosRankSum=1.472;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,25:106:99:286,0,1902
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1436 chr1 46313 . T A 271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.013;DP=108;Dels=0.00;FS=12.679;HaplotypeScore=73.9836;MLEAC=1;MLEAF=0.500;MQ=31.59;MQ0=13;MQRankSum=-1.299;QD=2.52;ReadPosRankSum=0.178;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:85,23:108:99:300,0,1934
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1437 chr1 46345 . G T 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.751;DP=118;Dels=0.00;FS=1.369;HaplotypeScore=15.7222;MLEAC=1;MLEAF=0.500;MQ=30.78;MQ0=12;MQRankSum=0.291;QD=2.25;ReadPosRankSum=1.341;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:95,23:118:99:294,0,1983
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1438 chr1 46349 . A G 370.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.226;DP=129;Dels=0.00;FS=0.000;HaplotypeScore=20.2580;MLEAC=1;MLEAF=0.500;MQ=32.38;MQ0=11;MQRankSum=4.078;QD=2.87;ReadPosRankSum=-1.669;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:107,22:129:99:399,0,2225
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1439 chr1 46360 . A G 330.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.738;DP=121;Dels=0.00;FS=0.000;HaplotypeScore=144.3890;MLEAC=1;MLEAF=0.500;MQ=34.17;MQ0=10;MQRankSum=-0.032;QD=2.73;ReadPosRankSum=0.335;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:96,25:121:99:359,0,2284
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|
|
1440 chr1 46365 . G T 168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.855;DP=118;Dels=0.00;FS=0.000;HaplotypeScore=86.2004;MLEAC=1;MLEAF=0.500;MQ=34.29;MQ0=10;MQRankSum=-0.261;QD=1.43;ReadPosRankSum=-0.928;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:99,19:118:99:197,0,2403
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|
|
1441 chr1 46370 . A G 351.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.186;DP=121;Dels=0.00;FS=0.988;HaplotypeScore=85.2005;MLEAC=1;MLEAF=0.500;MQ=35.94;MQ0=9;MQRankSum=3.941;QD=2.91;ReadPosRankSum=0.376;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:100,21:121:99:380,0,2395
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|
1442 chr1 46385 . A T 1987.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.564;DP=132;Dels=0.00;FS=0.000;HaplotypeScore=1.9946;MLEAC=1;MLEAF=0.500;MQ=41.86;MQ0=1;MQRankSum=-4.706;QD=15.06;ReadPosRankSum=0.577;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:54,78:132:99:2016,0,1639
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|
1443 chr1 46409 . G A 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.697;DP=147;Dels=0.00;FS=5.237;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.74;MQ0=1;MQRankSum=3.328;QD=4.48;ReadPosRankSum=2.209;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:119,28:147:99:687,0,3761
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|
|
1444 chr1 46413 . G A 5462.77 . AC=2;AF=1.00;AN=2;DP=150;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=45.19;MQ0=1;QD=31.52;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,150:150:99:5491,421,0
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|
|
1445 chr1 46441 . G A 5317.77 . AC=2;AF=1.00;AN=2;DP=134;Dels=0.00;FS=0.000;HaplotypeScore=24.9609;MLEAC=2;MLEAF=1.00;MQ=46.55;MQ0=1;QD=30.22;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,134:134:99:5346,400,0
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|
|
1446 chr1 46442 . A T 844.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=132;Dels=0.00;FS=6.626;HaplotypeScore=24.9609;MLEAC=1;MLEAF=0.500;MQ=46.74;MQ0=1;MQRankSum=0.945;QD=6.40;ReadPosRankSum=2.434;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:101,31:132:99:873,0,3591
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|
1447 chr1 46448 . T C 526.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.670;DP=120;Dels=0.00;FS=1.884;HaplotypeScore=45.9537;MLEAC=1;MLEAF=0.500;MQ=46.81;MQ0=1;MQRankSum=-1.356;QD=4.39;ReadPosRankSum=0.293;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:97,23:120:99:555,0,3478
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|
1448 chr1 46453 . T A 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=109;Dels=0.00;FS=3.408;HaplotypeScore=1.9892;MLEAC=1;MLEAF=0.500;MQ=47.07;MQ0=1;MQRankSum=-1.198;QD=4.26;ReadPosRankSum=1.024;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:89,20:109:99:493,0,3241
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1449 chr1 46466 . T A 1384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.022;DP=98;Dels=0.00;FS=1.650;HaplotypeScore=38.9441;MLEAC=1;MLEAF=0.500;MQ=46.96;MQ0=1;MQRankSum=0.510;QD=14.13;ReadPosRankSum=0.930;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:52,46:98:99:1413,0,1799
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|
|
1450 chr1 46486 . T A 874.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.311;DP=62;Dels=0.00;FS=0.975;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=43.40;MQ0=1;MQRankSum=-0.195;QD=14.11;ReadPosRankSum=-0.137;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,29:62:99:903,0,1128
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|
1451 chr1 46489 . A G 2225.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=2;MLEAF=1.00;MQ=42.98;MQ0=1;QD=30.18;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2254,175,0
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|
1452 chr1 46505 . T C 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.388;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=39.03;MQ0=0;MQRankSum=1.388;QD=8.99;ReadPosRankSum=-1.130;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:15,8:24:99:244,0,502
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|
1453 chr1 46511 . G C 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.761;DP=13;Dels=0.00;FS=2.920;HaplotypeScore=1.9890;MLEAC=1;MLEAF=0.500;MQ=36.55;MQ0=0;MQRankSum=0.592;QD=4.06;ReadPosRankSum=-1.099;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:10,3:13:81:81,0,328
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|
|
1454 chr1 46521 . C T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=2.9990;MLEAC=1;MLEAF=0.500;MQ=33.95;MQ0=0;MQRankSum=-0.198;QD=2.13;ReadPosRankSum=0.198;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:5,2:7:43:43,0,159
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|
1455 chr1 46524 . A C 63.23 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=2.9781;MLEAC=1;MLEAF=0.500;MQ=32.80;MQ0=0;QD=12.65;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:5:9:107,9,0
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|
|
1456 chr1 46567 . T C 942.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.84;MQ0=0;QD=28.57;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,33:33:81:971,81,0
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|
1457 chr1 46579 . T C 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.651;DP=54;Dels=0.00;FS=2.600;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=40.98;MQ0=0;MQRankSum=-0.248;QD=8.00;ReadPosRankSum=-0.266;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:36,18:54:99:460,0,1017
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|
1458 chr1 46608 . A G 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.810;DP=97;Dels=0.00;FS=7.798;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=45.77;MQ0=1;MQRankSum=0.169;QD=6.28;ReadPosRankSum=0.458;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:70,27:97:99:637,0,2291
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|
1459 chr1 46649 . C G 529.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.383;DP=128;Dels=0.00;FS=5.797;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=50.51;MQ0=1;MQRankSum=0.828;QD=4.14;ReadPosRankSum=-0.170;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:102,26:128:99:558,0,3425
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|
|
1460 chr1 46661 . T C 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.082;DP=123;Dels=0.00;FS=0.000;HaplotypeScore=1.8874;MLEAC=1;MLEAF=0.500;MQ=52.82;MQ0=1;MQRankSum=-1.890;QD=4.49;ReadPosRankSum=-0.533;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:98,25:123:99:580,0,3412
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|
1461 chr1 46669 . T C 309.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.271;DP=111;Dels=0.00;FS=0.000;HaplotypeScore=71.8527;MLEAC=1;MLEAF=0.500;MQ=54.24;MQ0=2;MQRankSum=-1.040;QD=2.79;ReadPosRankSum=0.046;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:94,17:111:99:338,0,3242
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|
1462 chr1 46672 . T C 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.735;DP=101;Dels=0.00;FS=1.153;HaplotypeScore=51.8777;MLEAC=1;MLEAF=0.500;MQ=55.02;MQ0=2;MQRankSum=0.285;QD=2.14;ReadPosRankSum=1.621;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:88,13:101:99:244,0,3052
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|
1463 chr1 46675 . C T 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.992;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=49.8785;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=2;MQRankSum=0.732;QD=1.80;ReadPosRankSum=2.032;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:88,12:100:99:208,0,3050
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|
1464 chr1 46676 . T C 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=65.8754;MLEAC=1;MLEAF=0.500;MQ=54.96;MQ0=2;MQRankSum=0.553;QD=1.87;ReadPosRankSum=1.978;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:87,12:99:99:213,0,3001
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|
1465 chr1 46677 . A G 505.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.866;DP=103;Dels=0.00;FS=3.208;HaplotypeScore=64.9814;MLEAC=1;MLEAF=0.500;MQ=54.76;MQ0=2;MQRankSum=-2.102;QD=4.91;ReadPosRankSum=0.977;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:79,24:103:99:534,0,2803
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|
1466 chr1 46680 . A G 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.424;DP=105;Dels=0.00;FS=3.142;HaplotypeScore=55.7727;MLEAC=1;MLEAF=0.500;MQ=54.17;MQ0=2;MQRankSum=-1.393;QD=4.65;ReadPosRankSum=1.009;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,23:105:99:516,0,2857
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|
1467 chr1 46706 . T A 186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.654;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=2.7898;MLEAC=1;MLEAF=0.500;MQ=51.38;MQ0=2;MQRankSum=0.757;QD=2.05;ReadPosRankSum=-0.339;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,17:91:99:215,0,2448
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|
1468 chr1 46718 . A C 1001.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.273;DP=81;Dels=0.00;FS=1.893;HaplotypeScore=14.9370;MLEAC=1;MLEAF=0.500;MQ=50.24;MQ0=2;MQRankSum=0.582;QD=12.37;ReadPosRankSum=1.963;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,34:81:99:1030,0,1456
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|
1469 chr1 46719 . A C 255.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.315;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=14.9370;MLEAC=1;MLEAF=0.500;MQ=50.24;MQ0=2;MQRankSum=0.250;QD=3.16;ReadPosRankSum=-0.404;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:66,15:81:99:284,0,2191
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|
1470 chr1 46726 . T C 2626.77 . AC=2;AF=1.00;AN=2;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=11.9384;MLEAC=2;MLEAF=1.00;MQ=49.53;MQ0=2;QD=34.56;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,75:76:99:2655,202,0
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|
1471 chr1 46731 . T C 2453.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.9987;MLEAC=2;MLEAF=1.00;MQ=48.88;MQ0=2;QD=34.08;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,72:72:99:2482,193,0
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|
1472 chr1 46759 . C A 1490.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=9.8664;MLEAC=2;MLEAF=1.00;MQ=36.57;MQ0=2;QD=28.13;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,53:53:99:1519,129,0
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|
1473 chr1 46779 . T A 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.055;DP=47;Dels=0.00;FS=2.615;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.41;MQ0=8;MQRankSum=-1.409;QD=0.34;ReadPosRankSum=-0.531;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,14:47:44:44,0,779
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|
1474 chr1 46829 . G A 136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.094;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.9157;MLEAC=1;MLEAF=0.500;MQ=28.31;MQ0=9;MQRankSum=-1.417;QD=3.18;ReadPosRankSum=-0.019;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,19:43:99:165,0,685
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|
1475 chr1 46863 . T A 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.612;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.6918;MLEAC=1;MLEAF=0.500;MQ=34.16;MQ0=4;MQRankSum=1.021;QD=3.19;ReadPosRankSum=-0.671;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,10:31:99:127,0,637
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|
1476 chr1 46875 . C T 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.178;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=33.74;MQ0=4;MQRankSum=0.391;QD=7.75;ReadPosRankSum=0.746;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,9:25:99:222,0,386
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|
1477 chr1 46877 . A G 192.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.036;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=33.74;MQ0=4;MQRankSum=-0.391;QD=7.71;ReadPosRankSum=0.675;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,9:25:99:221,0,382
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|
1478 chr1 46911 . T C 225.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=31.99;MQ0=4;MQRankSum=-0.295;QD=11.88;ReadPosRankSum=1.120;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,13:19:99:254,0,170
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|
1479 chr1 46912 . T C 139.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.237;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=31.99;MQ0=4;MQRankSum=-0.059;QD=7.36;ReadPosRankSum=-1.237;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,6:19:99:168,0,256
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|
1480 chr1 46921 . A T 131.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.473;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=31.99;MQ0=4;MQRankSum=1.120;QD=6.94;ReadPosRankSum=-1.237;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,6:19:99:160,0,232
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|
1481 chr1 46929 . T C 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.752;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=2.9987;MLEAC=1;MLEAF=0.500;MQ=30.25;MQ0=4;MQRankSum=1.826;QD=1.36;ReadPosRankSum=-1.396;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,2:16:50:50,0,263
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|
1482 chr1 46930 . T C 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.382;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=29.49;MQ0=4;MQRankSum=0.382;QD=2.05;ReadPosRankSum=-0.382;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:12,3:15:59:59,0,224
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|
1483 chr1 46932 . T G 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.597;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=29.49;MQ0=4;MQRankSum=-0.278;QD=10.05;ReadPosRankSum=0.597;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:4,11:15:99:179,0,100
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|
1484 chr1 47124 . A G 104.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.189;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=6.6461;MLEAC=1;MLEAF=0.500;MQ=28.99;MQ0=5;MQRankSum=2.616;QD=3.49;ReadPosRankSum=-0.713;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,5:30:99:133,0,417
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|
1485 chr1 47130 . C A 109.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.139;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=6.6461;MLEAC=1;MLEAF=0.500;MQ=28.99;MQ0=5;MQRankSum=-0.972;QD=3.54;ReadPosRankSum=-0.417;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,8:31:99:138,0,432
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|
1486 chr1 47133 . A T 171.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.968;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=15.5825;MLEAC=1;MLEAF=0.500;MQ=29.36;MQ0=5;MQRankSum=2.905;QD=5.37;ReadPosRankSum=-1.743;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,7:32:99:200,0,418
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1487 chr1 47143 . G A 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.890;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=8.6961;MLEAC=1;MLEAF=0.500;MQ=29.14;MQ0=5;MQRankSum=1.890;QD=0.78;ReadPosRankSum=1.736;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,3:33:54:54,0,575
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1488 chr1 47144 . A G 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.060;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=3.9886;MLEAC=1;MLEAF=0.500;MQ=29.14;MQ0=5;MQRankSum=1.440;QD=17.39;ReadPosRankSum=-0.420;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:7,26:33:45:602,0,45
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1489 chr1 47176 . T C 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.415;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=14.0311;MLEAC=1;MLEAF=0.500;MQ=29.24;MQ0=6;MQRankSum=-3.114;QD=8.56;ReadPosRankSum=-0.467;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:12,20:32:99:302,0,299
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1490 chr1 47177 . G A 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=14.0311;MLEAC=1;MLEAF=0.500;MQ=29.47;MQ0=6;MQRankSum=0.027;QD=6.93;ReadPosRankSum=0.356;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,11:31:99:243,0,342
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1491 chr1 47200 . T C 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.312;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.35;MQ0=1;MQRankSum=0.312;QD=7.13;ReadPosRankSum=1.954;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:7,7:14:99:128,0,187
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1492 chr1 47230 . T A 178.8 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=19.08;MQ0=3;QD=9.93;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,18:18:21:207,21,0
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1493 chr1 47234 . T C 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.630;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=20.58;MQ0=3;MQRankSum=-1.721;QD=2.61;ReadPosRankSum=1.721;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:8,13:21:83:83,0,132
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1494 chr1 47250 . G A 149.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.640;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=5.7510;MLEAC=1;MLEAF=0.500;MQ=21.76;MQ0=5;MQRankSum=-1.456;QD=2.27;ReadPosRankSum=0.646;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:44,22:66:99:178,0,749
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1495 chr1 47261 . A G 1410.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.543;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=6.7299;MLEAC=1;MLEAF=0.500;MQ=24.69;MQ0=5;MQRankSum=-5.094;QD=13.44;ReadPosRankSum=1.015;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,92:105:99:1439,0,288
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1496 chr1 47285 . A T 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.781;DP=169;Dels=0.00;FS=25.466;HaplotypeScore=47.9098;MLEAC=1;MLEAF=0.500;MQ=25.11;MQ0=7;MQRankSum=-4.336;QD=4.42;ReadPosRankSum=3.540;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:101,68:169:99:776,0,2136
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1497 chr1 47298 . G A 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.905;DP=190;Dels=0.00;FS=15.234;HaplotypeScore=62.4649;MLEAC=1;MLEAF=0.500;MQ=25.20;MQ0=9;MQRankSum=0.954;QD=0.07;ReadPosRankSum=-0.318;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:171,18:190:41:41,0,3305
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1498 chr1 47310 . A T 485.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.824;DP=205;Dels=0.00;FS=0.000;HaplotypeScore=49.7328;MLEAC=1;MLEAF=0.500;MQ=25.09;MQ0=7;MQRankSum=4.634;QD=2.37;ReadPosRankSum=0.186;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:176,29:205:99:514,0,2996
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1499 chr1 47323 . G A 1045.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.212;DP=211;Dels=0.00;FS=17.070;HaplotypeScore=51.7365;MLEAC=1;MLEAF=0.500;MQ=25.41;MQ0=8;MQRankSum=-0.372;QD=4.96;ReadPosRankSum=0.233;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:139,72:211:99:1074,0,2488
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1500 chr1 47338 . C T 938.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.180;DP=186;Dels=0.02;FS=12.473;HaplotypeScore=79.8806;MLEAC=1;MLEAF=0.500;MQ=25.59;MQ0=8;MQRankSum=-2.645;QD=5.05;ReadPosRankSum=-1.238;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:110,73:183:99:967,0,2144
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1501 chr1 47343 . A C 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.678;DP=175;Dels=0.00;FS=24.414;HaplotypeScore=63.4079;MLEAC=1;MLEAF=0.500;MQ=25.75;MQ0=8;MQRankSum=-4.741;QD=1.42;ReadPosRankSum=-2.918;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:123,52:175:99:276,0,2689
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1502 chr1 47371 . T C 1059.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.308;DP=89;Dels=0.00;FS=1.351;HaplotypeScore=13.6568;MLEAC=1;MLEAF=0.500;MQ=24.59;MQ0=7;MQRankSum=-0.275;QD=11.91;ReadPosRankSum=-0.593;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,70:89:99:1088,0,261
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1503 chr1 47393 . G A 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.335;DP=52;Dels=0.00;FS=11.083;HaplotypeScore=2.6277;MLEAC=1;MLEAF=0.500;MQ=22.57;MQ0=6;MQRankSum=-1.494;QD=0.31;ReadPosRankSum=1.210;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:41,11:52:44:44,0,511
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1504 chr1 47428 . T C 338.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.940;DP=69;Dels=0.00;FS=2.933;HaplotypeScore=8.8333;MLEAC=1;MLEAF=0.500;MQ=23.55;MQ0=5;MQRankSum=3.350;QD=4.91;ReadPosRankSum=0.000;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,22:69:99:367,0,707
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1505 chr1 47434 . T C 785.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.090;DP=72;Dels=0.00;FS=5.763;HaplotypeScore=21.1457;MLEAC=1;MLEAF=0.500;MQ=23.17;MQ0=5;MQRankSum=-4.249;QD=10.91;ReadPosRankSum=1.041;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:15,57:72:99:814,0,307
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1506 chr1 47443 . G A 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.058;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=18.3434;MLEAC=1;MLEAF=0.500;MQ=20.97;MQ0=15;MQRankSum=-0.420;QD=0.53;ReadPosRankSum=1.565;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,18:99:81:81,0,1206
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1507 chr1 47486 . T C 1453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.037;DP=155;Dels=0.00;FS=0.000;HaplotypeScore=12.8061;MLEAC=1;MLEAF=0.500;MQ=22.09;MQ0=28;MQRankSum=-5.676;QD=9.38;ReadPosRankSum=1.987;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:36,119:155:99:1482,0,780
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1508 chr1 47491 . T C 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.483;DP=156;Dels=0.00;FS=0.000;HaplotypeScore=17.2378;MLEAC=1;MLEAF=0.500;MQ=22.27;MQ0=26;MQRankSum=5.308;QD=3.06;ReadPosRankSum=-1.409;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:133,23:156:99:506,0,1813
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1509 chr1 47535 . C T 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.904;DP=93;Dels=0.02;FS=0.000;HaplotypeScore=38.1338;MLEAC=1;MLEAF=0.500;MQ=21.13;MQ0=22;MQRankSum=2.066;QD=3.23;ReadPosRankSum=1.772;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:73,16:91:99:329,0,900
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1510 chr1 47567 . G A 567.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.580;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=4.7649;MLEAC=2;MLEAF=1.00;MQ=23.23;MQ0=4;MQRankSum=0.223;QD=17.74;ReadPosRankSum=-1.561;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:6,26:32:31:596,31,0
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1511 chr1 47584 . T C 27.75 LowQual AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=13.33;MQ0=4;QD=4.62;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:4,2:6:6:55,6,0
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1512 chr1 47788 . G A 57.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.406;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=10.71;MQ0=14;MQRankSum=1.537;QD=2.86;ReadPosRankSum=0.406;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:17,3:20:9:85,9,0
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1513 chr1 47807 . T C 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.002;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=14.86;MQ0=12;MQRankSum=-1.709;QD=0.70;ReadPosRankSum=-2.534;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,18:27:47:47,0,128
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1514 chr1 47841 . C A 85.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.383;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=1.9157;MLEAC=1;MLEAF=0.500;MQ=15.69;MQ0=10;MQRankSum=0.024;QD=2.26;ReadPosRankSum=0.315;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,15:38:99:114,0,159
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1515 chr1 47868 . A G 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.408;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=14.6837;MLEAC=1;MLEAF=0.500;MQ=16.29;MQ0=5;MQRankSum=0.408;QD=1.05;ReadPosRankSum=0.168;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,10:33:63:63,0,165
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1516 chr1 47905 . T C 76.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.123;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.00;MQ=14.10;MQ0=0;MQRankSum=-0.919;QD=4.47;ReadPosRankSum=1.531;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,16:17:12:104,12,0
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1517 chr1 47908 . G C 76.03 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.35;MQ0=0;QD=5.07;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,15:15:12:104,12,0
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1518 chr1 48010 . C T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.319;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=9.5644;MLEAC=1;MLEAF=0.500;MQ=17.06;MQ0=4;MQRankSum=1.490;QD=1.24;ReadPosRankSum=1.149;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,5:32:68:68,0,115
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1519 chr1 48044 . T C 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.952;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=15.75;MQ0=6;MQRankSum=0.905;QD=2.20;ReadPosRankSum=1.323;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,12:34:99:103,0,101
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1520 chr1 48062 . T C 149.84 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.286;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=2;MLEAF=1.00;MQ=16.25;MQ0=3;MQRankSum=1.884;QD=5.99;ReadPosRankSum=0.171;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:4,21:25:18:178,18,0
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1521 chr1 48067 . T C 24.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.033;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=1.9664;MLEAC=1;MLEAF=0.500;MQ=16.25;MQ0=3;MQRankSum=-0.560;QD=0.99;ReadPosRankSum=-0.033;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,11:25:53:53,0,86
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1522 chr1 48077 . G A 10.33 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.200;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=11.66;MQ0=2;MQRankSum=0.000;QD=0.65;ReadPosRankSum=1.067;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,5:16:15:38,0,15
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1523 chr1 48103 . C T 10.33 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.365;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=13.51;MQ0=0;MQRankSum=0.000;QD=1.03;ReadPosRankSum=1.447;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,4:10:15:38,0,15
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1524 chr1 69651 . C A 54.28 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.77;MQ0=1;QD=6.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,8:8:9:82,9,0
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1525 chr1 69661 . T C 54.28 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=13.92;MQ0=2;QD=6.03;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,9:9:9:82,9,0
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1526 chr1 69674 . T C 54.28 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=13.92;MQ0=2;QD=6.03;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,9:9:9:82,9,0
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1527 chr1 69693 . C G 54.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.747;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.15;MQ0=2;MQRankSum=0.747;QD=5.43;ReadPosRankSum=0.747;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,9:10:9:82,9,0
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1528 chr1 69699 . C T 41.9 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.666;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.03;MQ0=2;MQRankSum=-0.762;QD=3.81;ReadPosRankSum=1.666;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:2,9:11:15:70,0,15
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1529 chr1 69764 . A G 449.56 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.331;DP=37;Dels=0.00;FS=9.031;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=23.29;MQ0=17;MQRankSum=2.126;QD=12.15;ReadPosRankSum=0.047;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,16:37:7:477,0,7
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1530 chr1 69840 . G A 581.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=2.6917;MLEAC=1;MLEAF=0.500;MQ=29.33;MQ0=7;MQRankSum=-2.507;QD=16.16;ReadPosRankSum=0.039;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:3,31:36:55:610,0,55
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1531 chr1 69869 . T C 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.277;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=30.44;MQ0=9;MQRankSum=-2.380;QD=0.76;ReadPosRankSum=1.273;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:35,11:46:63:63,0,767
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1532 chr1 69912 . A G 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.049;DP=89;Dels=0.00;FS=2.410;HaplotypeScore=43.2151;MLEAC=1;MLEAF=0.500;MQ=28.97;MQ0=20;MQRankSum=-2.202;QD=0.85;ReadPosRankSum=-1.327;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:71,18:89:99:104,0,1176
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1533 chr1 69914 . T A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.418;DP=89;Dels=0.00;FS=2.466;HaplotypeScore=31.1187;MLEAC=1;MLEAF=0.500;MQ=28.72;MQ0=20;MQRankSum=-2.123;QD=0.55;ReadPosRankSum=-0.877;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,15:89:77:77,0,1075
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1534 chr1 69917 . A G 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.757;DP=93;Dels=0.00;FS=4.107;HaplotypeScore=21.6983;MLEAC=1;MLEAF=0.500;MQ=28.07;MQ0=21;MQRankSum=6.024;QD=8.30;ReadPosRankSum=3.447;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:60,33:93:99:800,0,323
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1535 chr1 69936 . T C 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.032;DP=99;Dels=0.00;FS=7.704;HaplotypeScore=13.1641;MLEAC=1;MLEAF=0.500;MQ=29.72;MQ0=22;MQRankSum=-2.828;QD=0.58;ReadPosRankSum=-0.226;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,24:99:86:86,0,1391
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1536 chr1 69952 . G A 110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.715;DP=98;Dels=0.00;FS=10.410;HaplotypeScore=7.2476;MLEAC=1;MLEAF=0.500;MQ=31.15;MQ0=22;MQRankSum=-3.094;QD=1.13;ReadPosRankSum=1.550;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,23:98:99:139,0,1447
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|
1537 chr1 70044 . T C 383.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.831;DP=64;Dels=0.00;FS=17.302;HaplotypeScore=1.4972;MLEAC=1;MLEAF=0.500;MQ=39.43;MQ0=5;MQRankSum=-6.056;QD=6.00;ReadPosRankSum=-3.773;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:35,29:64:99:412,0,1246
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|
1538 chr1 70061 . A T 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.581;DP=133;Dels=0.00;FS=7.265;HaplotypeScore=20.7708;MLEAC=1;MLEAF=0.500;MQ=36.02;MQ0=7;MQRankSum=-0.379;QD=2.95;ReadPosRankSum=-1.067;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:108,25:133:99:420,0,2776
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|
1539 chr1 70083 . T A 2582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;DP=229;Dels=0.00;FS=16.594;HaplotypeScore=75.2516;MLEAC=1;MLEAF=0.500;MQ=35.83;MQ0=10;MQRankSum=-6.665;QD=11.28;ReadPosRankSum=-0.109;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:50,97:229:99:2611,0,1502
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|
1540 chr1 70125 . G T 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.317;DP=250;Dels=0.00;FS=22.446;HaplotypeScore=27.9709;MLEAC=1;MLEAF=0.500;MQ=34.24;MQ0=12;MQRankSum=6.009;QD=2.97;ReadPosRankSum=-1.398;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:216,34:250:99:771,0,5278
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|
|
1541 chr1 70150 . A T 2213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=239;Dels=0.00;FS=21.127;HaplotypeScore=368.1172;MLEAC=1;MLEAF=0.500;MQ=33.77;MQ0=11;MQRankSum=1.765;QD=9.26;ReadPosRankSum=0.325;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:156,83:239:99:2242,0,3406
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|
|
1542 chr1 70216 . A C 612.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=108;Dels=0.00;FS=9.502;HaplotypeScore=1.7297;MLEAC=1;MLEAF=0.500;MQ=29.27;MQ0=14;MQRankSum=-0.174;QD=5.67;ReadPosRankSum=-0.831;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:70,38:108:99:641,0,1179
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|
1543 chr1 70250 . G A 1741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.529;DP=135;Dels=0.00;FS=13.533;HaplotypeScore=55.9122;MLEAC=1;MLEAF=0.500;MQ=30.56;MQ0=13;MQRankSum=-4.770;QD=12.90;ReadPosRankSum=-1.687;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,110:135:99:1770,0,694
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|
1544 chr1 70260 . T A 1494.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.171;DP=159;Dels=0.00;FS=11.693;HaplotypeScore=60.0297;MLEAC=1;MLEAF=0.500;MQ=32.41;MQ0=12;MQRankSum=3.229;QD=9.40;ReadPosRankSum=-1.725;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:97,62:159:99:1523,0,1679
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|
1545 chr1 70302 . G C 22.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.849;DP=250;Dels=0.00;FS=0.000;HaplotypeScore=38.7004;MLEAC=1;MLEAF=0.500;MQ=30.81;MQ0=27;MQRankSum=2.779;QD=0.09;ReadPosRankSum=-0.062;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:234,14:250:51:51,0,4942
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|
1546 chr1 70324 . G A 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.298;DP=250;Dels=0.00;FS=0.000;HaplotypeScore=72.4821;MLEAC=1;MLEAF=0.500;MQ=30.43;MQ0=36;MQRankSum=-1.206;QD=1.62;ReadPosRankSum=-0.310;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:212,38:250:99:433,0,4781
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|
1547 chr1 70330 . T C 1073.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.778;DP=247;Dels=0.00;FS=0.000;HaplotypeScore=72.4821;MLEAC=1;MLEAF=0.500;MQ=29.87;MQ0=39;MQRankSum=4.681;QD=4.35;ReadPosRankSum=0.440;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:201,45:247:99:1102,0,3835
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1548 chr1 70352 . C T 944.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.133;DP=231;Dels=0.00;FS=0.000;HaplotypeScore=38.6164;MLEAC=1;MLEAF=0.500;MQ=29.11;MQ0=43;MQRankSum=-0.256;QD=4.09;ReadPosRankSum=1.173;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:164,67:231:99:973,0,3380
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1549 chr1 70354 . A G 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.510;DP=228;Dels=0.00;FS=0.000;HaplotypeScore=36.7869;MLEAC=1;MLEAF=0.500;MQ=28.93;MQ0=43;MQRankSum=0.019;QD=2.38;ReadPosRankSum=1.450;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:181,47:228:99:571,0,3676
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1550 chr1 70360 . A G 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.327;DP=214;Dels=0.00;FS=0.000;HaplotypeScore=31.5616;MLEAC=1;MLEAF=0.500;MQ=28.34;MQ0=42;MQRankSum=0.615;QD=3.26;ReadPosRankSum=0.618;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:163,51:214:99:725,0,3164
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1551 chr1 70400 . A G 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.039;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.22;MQ0=0;MQRankSum=-1.795;QD=15.51;ReadPosRankSum=0.535;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,14:23:99:385,0,241
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1552 chr1 70409 . T C 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.739;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.14;MQ0=0;MQRankSum=-2.381;QD=13.95;ReadPosRankSum=0.958;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,14:25:99:377,0,326
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1553 chr1 70454 . T A 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.499;DP=38;Dels=0.00;FS=4.521;HaplotypeScore=2.5142;MLEAC=1;MLEAF=0.500;MQ=46.06;MQ0=0;MQRankSum=-4.169;QD=10.55;ReadPosRankSum=0.264;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,17:38:99:429,0,678
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1554 chr1 70455 . G C 645.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.499;DP=38;Dels=0.00;FS=2.884;HaplotypeScore=1.7803;MLEAC=1;MLEAF=0.500;MQ=46.06;MQ0=0;MQRankSum=4.198;QD=16.99;ReadPosRankSum=-0.382;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,21:38:99:674,0,427
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1555 chr1 70467 . G A 1182.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=1.7803;MLEAC=2;MLEAF=1.00;MQ=47.26;MQ0=0;QD=33.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1211,99,0
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1556 chr1 70476 . C T 187.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.024;DP=28;Dels=0.00;FS=1.583;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.00;MQ0=0;MQRankSum=-4.339;QD=6.71;ReadPosRankSum=-2.613;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,10:28:99:216,0,597
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1557 chr1 70481 . T A 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.212;DP=29;Dels=0.00;FS=3.696;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.39;MQ0=0;MQRankSum=-4.266;QD=5.23;ReadPosRankSum=-2.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,9:29:99:180,0,720
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1558 chr1 70487 . G A 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.402;DP=31;Dels=0.00;FS=7.186;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.09;MQ0=0;MQRankSum=-3.992;QD=3.25;ReadPosRankSum=-0.685;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,7:31:99:129,0,866
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|
1559 chr1 70488 . G C 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.493;DP=30;Dels=0.00;FS=12.454;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.88;MQ0=0;MQRankSum=-3.759;QD=3.33;ReadPosRankSum=-0.026;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,6:30:99:128,0,824
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1560 chr1 70508 . A G 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.961;DP=31;Dels=0.00;FS=8.915;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.10;MQ0=0;MQRankSum=3.902;QD=21.83;ReadPosRankSum=2.250;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,20:31:99:705,0,304
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1561 chr1 70513 . T C 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.673;DP=29;Dels=0.00;FS=6.306;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=52.84;MQ0=0;MQRankSum=-3.512;QD=7.10;ReadPosRankSum=-0.966;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,9:29:99:234,0,716
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1562 chr1 70534 . A T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.500;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.15;MQ0=0;MQRankSum=4.082;QD=15.43;ReadPosRankSum=1.082;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,20:41:99:661,0,570
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1563 chr1 70544 . T C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.245;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.74;MQ0=0;MQRankSum=-3.969;QD=13.14;ReadPosRankSum=0.202;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,24:47:99:646,0,706
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1564 chr1 70546 . C G 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.867;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.85;MQ0=0;MQRankSum=-3.859;QD=14.29;ReadPosRankSum=0.413;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,25:48:99:714,0,704
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1565 chr1 70565 . A G 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.227;DP=52;Dels=0.00;FS=5.964;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.21;MQ0=0;MQRankSum=-2.949;QD=14.94;ReadPosRankSum=2.436;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,27:52:99:805,0,789
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|
1566 chr1 70576 . T C 838.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.260;DP=58;Dels=0.00;FS=5.843;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=48.49;MQ0=0;MQRankSum=-3.297;QD=14.46;ReadPosRankSum=2.442;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,29:58:99:867,0,930
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|
1567 chr1 70628 . T G 997.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.810;DP=62;Dels=0.00;FS=3.540;HaplotypeScore=4.7315;MLEAC=1;MLEAF=0.500;MQ=52.03;MQ0=0;MQRankSum=-0.331;QD=16.09;ReadPosRankSum=0.416;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:30,32:62:99:1026,0,961
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1568 chr1 70637 . G A 979.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.487;DP=57;Dels=0.00;FS=1.010;HaplotypeScore=4.7315;MLEAC=1;MLEAF=0.500;MQ=53.93;MQ0=0;MQRankSum=0.813;QD=17.19;ReadPosRankSum=-0.748;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,30:57:99:1008,0,828
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1569 chr1 70655 . A G 889.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.777;DP=53;Dels=0.00;FS=1.090;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=-0.769;QD=16.79;ReadPosRankSum=-2.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,27:53:99:918,0,834
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1570 chr1 70662 . T G 2101.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9947;MLEAC=2;MLEAF=1.00;MQ=56.72;MQ0=0;QD=34.63;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2130,160,0
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|
1571 chr1 70684 . C T 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.290;DP=57;Dels=0.00;FS=3.772;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=57.81;MQ0=1;MQRankSum=1.273;QD=17.59;ReadPosRankSum=-0.173;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1031,0,872
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|
1572 chr1 70716 . A G 976.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.361;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.79;MQ0=1;MQRankSum=-0.680;QD=16.01;ReadPosRankSum=-0.621;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,32:61:99:1005,0,945
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1573 chr1 70722 . G A 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.241;DP=64;Dels=0.00;FS=0.968;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.90;MQ0=1;MQRankSum=-0.310;QD=14.48;ReadPosRankSum=0.901;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,30:64:99:955,0,1044
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1574 chr1 70732 . T G 1039.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.942;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=1;MQRankSum=0.419;QD=16.25;ReadPosRankSum=0.186;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,32:64:99:1068,0,1033
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1575 chr1 70757 . A G 1003.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.027;DP=57;Dels=0.00;FS=2.307;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.09;MQ0=2;MQRankSum=0.704;QD=17.61;ReadPosRankSum=-0.908;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1032,0,802
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1576 chr1 70801 . T C 1321.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.33;MQ0=1;QD=31.86;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1350,102,0
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|
1577 chr1 70805 . T C 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.701;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=1;MQRankSum=-0.638;QD=11.39;ReadPosRankSum=3.331;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,14:35:99:427,0,704
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1578 chr1 70806 . G A 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.168;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=1;MQRankSum=-0.632;QD=11.19;ReadPosRankSum=3.192;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,14:36:99:431,0,755
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|
1579 chr1 70808 . T C 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.418;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=1;MQRankSum=-0.461;QD=11.99;ReadPosRankSum=2.671;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,14:34:99:436,0,682
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|
1580 chr1 70814 . A T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.018;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=1;MQRankSum=-0.281;QD=14.22;ReadPosRankSum=1.333;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,20:44:99:654,0,779
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|
1581 chr1 70860 . G C 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.800;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.732;QD=15.72;ReadPosRankSum=-0.025;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,28:55:99:893,0,931
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|
1582 chr1 70872 . A T 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.237;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.806;QD=14.49;ReadPosRankSum=-0.247;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,28:57:99:854,0,1019
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1583 chr1 70927 . T A 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.729;DP=54;Dels=0.00;FS=2.239;HaplotypeScore=28.8784;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.885;QD=15.03;ReadPosRankSum=0.833;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,25:54:99:840,0,984
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|
1584 chr1 70928 . C T 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.069;DP=54;Dels=0.00;FS=2.239;HaplotypeScore=28.8784;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.173;QD=14.92;ReadPosRankSum=0.642;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,25:54:99:834,0,975
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|
1585 chr1 70958 . G A 884.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.312;DP=57;Dels=0.00;FS=1.019;HaplotypeScore=3.9961;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=-0.008;QD=15.52;ReadPosRankSum=-0.855;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:30,27:57:99:913,0,1033
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|
|
1586 chr1 70978 . A C 1879.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.75;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1908,144,0
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|
1587 chr1 71024 . T A 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.209;QD=10.97;ReadPosRankSum=0.418;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,15:38:99:445,0,742
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|
|
1588 chr1 71043 . A G 412.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.014;DP=38;Dels=0.00;FS=1.271;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.530;QD=10.86;ReadPosRankSum=-0.257;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,14:38:99:441,0,841
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|
|
1589 chr1 71062 . G A 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.996;DP=39;Dels=0.00;FS=9.774;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.61;MQ0=0;MQRankSum=-1.775;QD=10.92;ReadPosRankSum=-1.342;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,15:39:99:454,0,819
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|
|
1590 chr1 71078 . A G 328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.024;DP=46;Dels=0.00;FS=9.879;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=0;MQRankSum=-2.684;QD=7.15;ReadPosRankSum=1.952;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,13:46:99:357,0,1152
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|
|
1591 chr1 71081 . T G 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.538;DP=45;Dels=0.00;FS=9.686;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=0;MQRankSum=-2.992;QD=7.59;ReadPosRankSum=1.991;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,13:45:99:370,0,1120
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|
1592 chr1 71151 . T C 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=48;Dels=0.00;FS=6.211;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=-0.755;QD=14.79;ReadPosRankSum=0.962;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,22:48:99:738,0,906
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|
|
1593 chr1 71164 . T G 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.534;DP=52;Dels=0.00;FS=5.816;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.829;QD=13.75;ReadPosRankSum=2.635;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,23:52:99:743,0,987
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|
1594 chr1 71175 . C T 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.190;DP=49;Dels=0.00;FS=8.135;HaplotypeScore=1.5661;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.410;QD=15.79;ReadPosRankSum=2.570;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,24:49:99:802,0,806
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|
1595 chr1 71183 . G A 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.428;DP=50;Dels=0.00;FS=5.868;HaplotypeScore=1.5661;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=-0.740;QD=13.42;ReadPosRankSum=3.290;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,23:50:99:699,0,927
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|
1596 chr1 71188 . T C 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=50;Dels=0.00;FS=4.061;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=-1.246;QD=13.50;ReadPosRankSum=2.647;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,23:50:99:703,0,954
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|
1597 chr1 71222 . A C 1672.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=2.6203;MLEAC=2;MLEAF=1.00;MQ=59.27;MQ0=0;QD=26.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1701,129,0
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1598 chr1 71229 . C T 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.374;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-1.588;QD=9.33;ReadPosRankSum=-2.495;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,14:42:99:420,0,1008
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|
1599 chr1 71244 . A T 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.387;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-2.527;QD=4.99;ReadPosRankSum=-1.716;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,8:37:99:213,0,1037
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1600 chr1 71245 . C T 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.080;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-3.757;QD=4.10;ReadPosRankSum=-1.239;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,7:36:99:176,0,1059
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1601 chr1 71254 . G T 68.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.549;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-3.568;QD=1.91;ReadPosRankSum=-0.412;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,5:36:97:97,0,1070
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1602 chr1 71258 . C T 1176.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;QD=34.61;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1205,99,0
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1603 chr1 71280 . T C 924.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,26:26:75:953,75,0
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1604 chr1 71284 . T C 956.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:985,78,0
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1605 chr1 71319 . G A 770.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:799,63,0
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1606 chr1 71344 . G C 750.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.92;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:779,60,0
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1607 chr1 71359 . G T 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.564;DP=32;Dels=0.00;FS=18.730;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.56;MQ0=0;MQRankSum=-4.690;QD=8.59;ReadPosRankSum=-1.888;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:303,0,699
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1608 chr1 71365 . A G 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.699;DP=30;Dels=0.00;FS=15.204;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.18;MQ0=0;MQRankSum=-4.593;QD=9.83;ReadPosRankSum=-1.037;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:323,0,626
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1609 chr1 71371 . C T 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=34;Dels=0.00;FS=14.526;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-4.775;QD=8.11;ReadPosRankSum=0.414;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,12:34:99:304,0,729
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1610 chr1 71381 . C T 293.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.304;DP=32;Dels=0.00;FS=11.957;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.56;MQ0=0;MQRankSum=-4.690;QD=9.18;ReadPosRankSum=2.316;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:322,0,668
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1611 chr1 71388 . T C 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.747;DP=35;Dels=0.00;FS=18.303;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.04;MQ0=0;MQRankSum=-4.813;QD=8.08;ReadPosRankSum=3.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:311,0,784
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1612 chr1 71570 . G A 897.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=61.40;MQ0=0;QD=31.63;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:926,69,0
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1613 chr1 71608 . A G 632.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=61.26;MQ0=0;QD=28.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:661,51,0
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1614 chr1 71631 . G A 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.385;DP=24;Dels=0.00;FS=16.510;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-4.055;QD=11.37;ReadPosRankSum=-2.981;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,9:24:99:301,0,519
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1615 chr1 71646 . A G 281.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.949;DP=21;Dels=0.00;FS=9.840;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=0;MQRankSum=-3.873;QD=13.42;ReadPosRankSum=-0.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,9:21:99:310,0,392
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1616 chr1 71649 . C T 283.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.292;DP=20;Dels=0.00;FS=10.263;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.18;MQ0=0;MQRankSum=-3.799;QD=14.19;ReadPosRankSum=-0.380;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,9:20:99:312,0,385
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1617 chr1 71668 . T C 152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.732;DP=22;Dels=0.00;FS=9.185;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=-3.575;QD=6.94;ReadPosRankSum=2.617;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:181,0,541
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1618 chr1 71670 . C T 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.518;DP=21;Dels=0.00;FS=12.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.16;MQ0=0;MQRankSum=-3.542;QD=7.42;ReadPosRankSum=2.997;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,6:21:99:184,0,526
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1619 chr1 71673 . T C 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.627;DP=22;Dels=0.00;FS=9.185;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=-3.575;QD=6.72;ReadPosRankSum=3.502;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:176,0,563
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1620 chr1 71675 . T C 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;DP=22;Dels=0.00;FS=9.185;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=-3.575;QD=6.63;ReadPosRankSum=3.502;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:174,0,568
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1621 chr1 71676 . A G 137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.455;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-3.606;QD=5.99;ReadPosRankSum=3.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,6:23:99:166,0,592
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1622 chr1 71693 . T G 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.595;DP=27;Dels=0.00;FS=8.671;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=-3.703;QD=4.03;ReadPosRankSum=1.895;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,6:27:99:137,0,745
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1623 chr1 71715 . A T 618.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.94;MQ0=0;QD=27.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:647,48,0
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1624 chr1 71716 . A T 611.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.94;MQ0=0;QD=32.79;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:640,48,0
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1625 chr1 71717 . A T 625.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.94;MQ0=0;QD=35.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:654,48,0
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1626 chr1 71718 . A T 704.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.94;MQ0=0;QD=28.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:733,54,0
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1627 chr1 71734 . G A 950.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.031;DP=49;Dels=0.00;FS=6.300;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.35;MQ0=1;MQRankSum=2.206;QD=19.40;ReadPosRankSum=2.478;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,28:49:99:979,0,585
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1628 chr1 71751 . T C 1954.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.88;MQ0=1;QD=30.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:1983,147,0
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1629 chr1 71752 . T C 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.360;DP=52;Dels=0.00;FS=8.561;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.88;MQ0=1;MQRankSum=-0.751;QD=11.90;ReadPosRankSum=0.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,23:52:99:647,0,1034
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1630 chr1 71768 . T G 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.210;DP=50;Dels=0.00;FS=6.439;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.40;MQ0=1;MQRankSum=0.630;QD=13.48;ReadPosRankSum=1.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,26:50:99:702,0,834
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1631 chr1 71769 . T C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.217;DP=48;Dels=0.00;FS=6.329;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.08;MQ0=0;MQRankSum=-0.010;QD=13.47;ReadPosRankSum=1.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,24:48:99:675,0,839
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1632 chr1 71772 . C T 1772.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9984;MLEAC=2;MLEAF=1.00;MQ=58.12;MQ0=0;QD=30.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1801,135,0
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1633 chr1 71809 . A C 2024.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=57.48;MQ0=1;QD=30.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2053,153,0
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1634 chr1 71829 . C A 1066.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.182;DP=56;Dels=0.00;FS=2.400;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.46;MQ0=1;MQRankSum=0.563;QD=19.05;ReadPosRankSum=-0.442;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,35:56:99:1095,0,684
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1635 chr1 71834 . T C 1044.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.637;DP=51;Dels=0.00;FS=2.568;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.86;MQ0=1;MQRankSum=0.212;QD=20.49;ReadPosRankSum=-0.758;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,33:51:99:1073,0,570
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|
1636 chr1 71853 . T C 942.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.834;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=55.00;MQ0=1;MQRankSum=-0.422;QD=19.24;ReadPosRankSum=0.084;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,30:49:99:971,0,612
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|
|
1637 chr1 71859 . G A 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.824;DP=49;Dels=0.00;FS=1.079;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=1;MQRankSum=-1.148;QD=16.89;ReadPosRankSum=1.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:856,0,696
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|
1638 chr1 71860 . A T 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.606;DP=48;Dels=0.00;FS=1.133;HaplotypeScore=2.9994;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=1;MQRankSum=-0.374;QD=17.77;ReadPosRankSum=1.423;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,27:48:99:881,0,668
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|
|
1639 chr1 71878 . T C 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.614;DP=44;Dels=0.00;FS=2.696;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=1;MQRankSum=-1.741;QD=16.99;ReadPosRankSum=1.619;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:776,0,611
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|
|
1640 chr1 71879 . G T 755.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.817;DP=45;Dels=0.00;FS=2.750;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=52.60;MQ0=1;MQRankSum=-1.880;QD=16.79;ReadPosRankSum=1.786;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,24:45:99:784,0,584
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1641 chr1 71900 . G A 544.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.234;DP=39;Dels=0.00;FS=6.884;HaplotypeScore=26.2859;MLEAC=1;MLEAF=0.500;MQ=50.73;MQ0=0;MQRankSum=0.829;QD=13.97;ReadPosRankSum=-0.126;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:573,0,657
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1642 chr1 71921 . G C 513.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=44.24;MQ0=0;QD=27.04;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,19:19:42:542,42,0
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|
1643 chr1 71950 . T A 90.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.058;DP=28;Dels=0.00;FS=21.924;HaplotypeScore=4.3987;MLEAC=1;MLEAF=0.500;MQ=32.58;MQ0=2;MQRankSum=-0.462;QD=3.24;ReadPosRankSum=-1.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:119,0,331
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1644 chr1 71973 . C A 115.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.018;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=5.0534;MLEAC=1;MLEAF=0.500;MQ=13.29;MQ0=15;MQRankSum=2.752;QD=1.90;ReadPosRankSum=3.058;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:54,7:61:75:144,0,75
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1645 chr1 71995 . C T 106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.495;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=22.9908;MLEAC=1;MLEAF=0.500;MQ=14.13;MQ0=18;MQRankSum=2.453;QD=1.44;ReadPosRankSum=3.369;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:66,8:74:99:135,0,173
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1646 chr1 72037 . G A 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.481;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=8.0800;MLEAC=1;MLEAF=0.500;MQ=11.16;MQ0=17;MQRankSum=2.289;QD=0.63;ReadPosRankSum=2.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:61,2:63:68:68,0,74
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1647 chr1 72059 . T C 106.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.241;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=1.7351;MLEAC=2;MLEAF=1.00;MQ=11.90;MQ0=9;MQRankSum=1.061;QD=2.65;ReadPosRankSum=-2.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:9,31:40:12:134,12,0
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1648 chr1 72137 . C T 135.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.983;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.91;MQ0=6;MQRankSum=3.138;QD=5.63;ReadPosRankSum=0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:16,7:24:12:163,12,0
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1649 chr1 72198 . A G 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.408;DP=34;Dels=0.03;FS=0.000;HaplotypeScore=32.2822;MLEAC=1;MLEAF=0.500;MQ=18.40;MQ0=8;MQRankSum=0.642;QD=0.79;ReadPosRankSum=-0.803;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,3:33:55:55,0,194
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1650 chr1 72220 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.957;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=8.1644;MLEAC=1;MLEAF=0.500;MQ=16.77;MQ0=8;MQRankSum=2.009;QD=1.02;ReadPosRankSum=2.679;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,3:33:62:62,0,141
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1651 chr1 72245 . G A 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.574;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=3.7817;MLEAC=1;MLEAF=0.500;MQ=17.26;MQ0=4;MQRankSum=1.052;QD=0.99;ReadPosRankSum=-1.148;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,3:30:58:58,0,156
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1652 chr1 72246 . G T 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.144;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=3.7817;MLEAC=1;MLEAF=0.500;MQ=17.26;MQ0=4;MQRankSum=2.261;QD=0.99;ReadPosRankSum=-0.625;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,2:30:58:58,0,154
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|
1653 chr1 72269 . T C 18.83 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.122;DP=23;Dels=0.00;FS=4.771;HaplotypeScore=5.5051;MLEAC=1;MLEAF=0.500;MQ=11.28;MQ0=6;MQRankSum=-0.537;QD=0.82;ReadPosRankSum=2.293;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,7:23:39:47,0,39
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|
1654 chr1 72271 . T C 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=22;Dels=0.00;FS=4.771;HaplotypeScore=4.7711;MLEAC=1;MLEAF=0.500;MQ=11.53;MQ0=6;MQRankSum=1.799;QD=0.51;ReadPosRankSum=-1.905;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,10:22:39:39,0,47
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|
1655 chr1 72309 . T G 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.537;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=9.6153;MLEAC=1;MLEAF=0.500;MQ=23.14;MQ0=3;MQRankSum=2.041;QD=2.45;ReadPosRankSum=-0.107;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:13,2:15:65:65,0,114
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1656 chr1 72313 . C T 65.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.788;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=12.8714;MLEAC=1;MLEAF=0.500;MQ=23.14;MQ0=3;MQRankSum=-1.000;QD=4.38;ReadPosRankSum=2.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:6,9:15:86:94,0,86
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1657 chr1 72362 . A G 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.365;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=21.15;MQ0=4;MQRankSum=0.000;QD=3.98;ReadPosRankSum=0.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:8,6:14:61:84,0,61
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|
1658 chr1 72457 . T G 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.362;DP=19;Dels=0.00;FS=3.979;HaplotypeScore=10.4309;MLEAC=1;MLEAF=0.500;MQ=16.41;MQ0=1;MQRankSum=-0.453;QD=0.68;ReadPosRankSum=2.174;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,8:19:41:41,0,92
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|
1659 chr1 72490 . A G 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.601;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=17.81;MQ0=2;MQRankSum=2.538;QD=5.57;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:13,11:24:54:162,0,54
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|
1660 chr1 72511 . C T 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.336;DP=23;Dels=0.00;FS=3.424;HaplotypeScore=8.8927;MLEAC=1;MLEAF=0.500;MQ=21.05;MQ0=2;MQRankSum=2.216;QD=0.61;ReadPosRankSum=-2.336;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,2:23:42:42,0,231
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|
1661 chr1 72546 . G A 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.714;DP=18;Dels=0.00;FS=3.010;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=22.48;MQ0=2;MQRankSum=2.143;QD=0.77;ReadPosRankSum=0.873;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,2:18:42:42,0,183
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|
1662 chr1 72554 . C T 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.086;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.6643;MLEAC=1;MLEAF=0.500;MQ=24.02;MQ0=2;MQRankSum=2.073;QD=1.59;ReadPosRankSum=1.678;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:13,2:15:52:52,0,163
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|
1663 chr1 72558 . C T 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.600;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=2.4964;MLEAC=1;MLEAF=0.500;MQ=22.45;MQ0=2;MQRankSum=0.289;QD=1.91;ReadPosRankSum=1.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:10,4:14:55:55,0,130
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|
1664 chr1 72562 . G A 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.271;DP=12;Dels=0.00;FS=8.751;HaplotypeScore=4.2846;MLEAC=1;MLEAF=0.500;MQ=22.65;MQ0=2;MQRankSum=1.271;QD=2.23;ReadPosRankSum=1.733;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:10,2:12:55:55,0,77
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1665 chr1 72602 . G A 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.822;DP=19;Dels=0.00;FS=10.000;HaplotypeScore=6.4109;MLEAC=1;MLEAF=0.500;MQ=20.13;MQ0=4;MQRankSum=1.734;QD=1.88;ReadPosRankSum=-0.456;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,2:19:64:64,0,89
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1666 chr1 72626 . T C 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.482;DP=23;Dels=0.00;FS=3.332;HaplotypeScore=8.3126;MLEAC=1;MLEAF=0.500;MQ=18.76;MQ0=5;MQRankSum=0.796;QD=2.34;ReadPosRankSum=0.515;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,6:23:82:82,0,124
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1667 chr1 72630 . G A 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=11.7259;MLEAC=1;MLEAF=0.500;MQ=18.34;MQ0=5;MQRankSum=0.787;QD=1.32;ReadPosRankSum=-1.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,9:24:60:60,0,147
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1668 chr1 72631 . T C 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.646;DP=25;Dels=0.00;FS=2.680;HaplotypeScore=11.7259;MLEAC=1;MLEAF=0.500;MQ=18.06;MQ0=5;MQRankSum=1.905;QD=2.15;ReadPosRankSum=0.106;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,3:25:82:82,0,124
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1669 chr1 72638 . A G 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=22.7383;MLEAC=1;MLEAF=0.500;MQ=17.66;MQ0=5;MQRankSum=-0.417;QD=3.96;ReadPosRankSum=-0.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,17:29:95:143,0,95
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1670 chr1 72646 . G A 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=2.219;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=9.5448;MLEAC=1;MLEAF=0.500;MQ=18.45;MQ0=5;MQRankSum=1.020;QD=0.60;ReadPosRankSum=1.080;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,9:33:48:48,0,249
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1671 chr1 72647 . A T 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.883;DP=33;Dels=0.00;FS=2.141;HaplotypeScore=9.5448;MLEAC=1;MLEAF=0.500;MQ=18.45;MQ0=5;MQRankSum=-1.102;QD=2.24;ReadPosRankSum=-1.315;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,12:33:99:102,0,158
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1672 chr1 72688 . A C 22.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.304;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=8.2417;MLEAC=1;MLEAF=0.500;MQ=17.84;MQ0=5;MQRankSum=0.604;QD=0.76;ReadPosRankSum=-0.986;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,9:30:51:51,0,209
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1673 chr1 72693 . A G,T 93.3 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.315;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=3.4300;MLEAC=1,1;MLEAF=0.500,0.500;MQ=17.69;MQ0=3;MQRankSum=0.315;QD=4.06;ReadPosRankSum=0.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/2:3,13,7:23:82:195,82,86,97,0,107
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1674 chr1 72717 . T C 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.369;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=2.4530;MLEAC=1;MLEAF=0.500;MQ=16.28;MQ0=1;MQRankSum=0.555;QD=3.41;ReadPosRankSum=-0.660;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:7,7:14:32:76,0,32
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1675 chr1 72825 . G C 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.250;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=6.6451;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=20;MQRankSum=1.350;QD=1.40;ReadPosRankSum=1.050;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:33,4:39:83:83,0,118
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|
1676 chr1 72829 . C T 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.750;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=6.6451;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=20;MQRankSum=1.050;QD=1.40;ReadPosRankSum=1.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:35,4:39:83:83,0,121
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|
1677 chr1 72855 . A G 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.464;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=16.6819;MLEAC=1;MLEAF=0.500;MQ=16.39;MQ0=10;MQRankSum=-0.705;QD=0.45;ReadPosRankSum=-1.464;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,14:27:40:40,0,130
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|
|
1678 chr1 72858 . G A 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.321;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=11.8688;MLEAC=1;MLEAF=0.500;MQ=16.70;MQ0=9;MQRankSum=1.415;QD=2.30;ReadPosRankSum=0.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,4:26:82:88,0,82
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|
|
1679 chr1 72865 . G A 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.456;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=9.3724;MLEAC=1;MLEAF=0.500;MQ=17.99;MQ0=8;MQRankSum=1.004;QD=0.55;ReadPosRankSum=0.091;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,3:22:40:40,0,130
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|
|
1680 chr1 72880 . C T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.386;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=20.39;MQ0=5;MQRankSum=-0.546;QD=0.99;ReadPosRankSum=-1.214;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:8,7:15:43:43,0,103
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|
|
1681 chr1 72889 . T A 11.83 LowQual AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=21.37;MQ0=0;QD=2.96;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,4:4:3:38,3,0
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|
|
1682 chr1 73036 . T A 208.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.62;MQ0=0;QD=34.81;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:237,18,0
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|
|
1683 chr1 73048 . A G 266.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.49;MQ0=0;QD=33.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:295,24,0
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|
|
1684 chr1 73057 . T C 276.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.49;MQ0=0;QD=34.60;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:305,24,0
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|
|
1685 chr1 73065 . G A 343.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.86;MQ0=0;QD=34.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:372,30,0
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|
|
1686 chr1 73081 . G A 317.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.59;MQ0=1;QD=28.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,11:11:27:346,27,0
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|
|
1687 chr1 73149 . G C 249.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.69;MQ0=0;QD=31.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:278,21,0
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|
|
1688 chr1 73163 . A G 322.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.65;MQ0=0;QD=26.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,9:9:27:351,27,0
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|
|
1689 chr1 73175 . G C 322.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.65;MQ0=0;QD=27.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,9:9:27:351,27,0
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|
|
1690 chr1 73190 . T C 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.190;DP=32;Dels=0.00;FS=5.979;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.22;MQ0=1;MQRankSum=-0.021;QD=8.71;ReadPosRankSum=4.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:307,0,753
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|
|
1691 chr1 73232 . T G 932.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.099;DP=44;Dels=0.00;FS=1.263;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.025;QD=21.20;ReadPosRankSum=1.585;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,29:44:99:961,0,450
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|
|
1692 chr1 73255 . T C 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.483;DP=47;Dels=0.00;FS=6.570;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=-2.077;QD=9.48;ReadPosRankSum=-0.977;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,16:47:99:474,0,1089
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|
|
1693 chr1 73261 . C A 962.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.379;DP=44;Dels=0.00;FS=4.722;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-0.183;QD=21.88;ReadPosRankSum=1.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,28:44:99:991,0,472
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|
|
1694 chr1 73263 . C G 937.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;DP=44;Dels=0.00;FS=2.932;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-1.964;QD=21.31;ReadPosRankSum=1.671;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,28:44:99:966,0,458
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|
|
1695 chr1 73275 . C T 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.486;DP=44;Dels=0.00;FS=1.263;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-1.535;QD=22.72;ReadPosRankSum=0.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,29:44:99:1028,0,450
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|
|
1696 chr1 73316 . C T 2034.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.40;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2063,157,0
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|
|
1697 chr1 73353 . T C 558.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.342;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.881;QD=11.40;ReadPosRankSum=-2.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:587,0,1121
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|
1698 chr1 73399 . A G 527.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.278;DP=55;Dels=0.00;FS=1.104;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=2.735;QD=9.60;ReadPosRankSum=2.215;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:37,18:55:99:556,0,1319
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|
1699 chr1 73405 . A T 1043.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.503;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=0.482;QD=21.30;ReadPosRankSum=-0.975;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,30:49:99:1072,0,626
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1700 chr1 73409 . A G 963.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.120;DP=50;Dels=0.00;FS=1.111;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-1.396;QD=19.28;ReadPosRankSum=-0.295;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:992,0,686
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1701 chr1 73415 . A C 823.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.654;DP=46;Dels=0.00;FS=2.689;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=-0.221;QD=17.91;ReadPosRankSum=0.198;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:852,0,629
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1702 chr1 73486 . T A 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.399;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.8288;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.472;QD=15.77;ReadPosRankSum=0.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:864,0,913
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|
1703 chr1 73498 . T G 985.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.429;DP=60;Dels=0.00;FS=7.060;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.598;QD=16.43;ReadPosRankSum=-1.035;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,31:60:99:1014,0,976
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1704 chr1 73526 . G C 1037.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.141;DP=55;Dels=0.00;FS=5.479;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=0.947;QD=18.87;ReadPosRankSum=-1.408;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1066,0,776
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1705 chr1 73533 . G A 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.024;DP=53;Dels=0.00;FS=1.107;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=1.014;QD=17.51;ReadPosRankSum=0.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,30:53:99:956,0,715
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|
1706 chr1 73553 . C T 2145.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.7338;MLEAC=2;MLEAF=1.00;MQ=59.48;MQ0=0;QD=31.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2174,160,0
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1707 chr1 73559 . G C 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.866;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.050;QD=12.94;ReadPosRankSum=-2.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:33,23:56:99:753,0,1151
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1708 chr1 73601 . T C 1170.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.426;DP=64;Dels=0.00;FS=0.969;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=0.995;QD=18.29;ReadPosRankSum=-0.142;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,36:64:99:1199,0,892
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1709 chr1 73621 . C T 1271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.511;DP=67;Dels=0.00;FS=0.922;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=1.292;QD=18.98;ReadPosRankSum=-0.019;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,37:67:99:1300,0,965
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1710 chr1 73648 . A G 935.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.955;DP=69;Dels=0.00;FS=2.001;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=-0.776;QD=13.56;ReadPosRankSum=0.391;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:37,32:69:99:964,0,1308
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1711 chr1 73726 . T A 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.877;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=1.512;QD=18.38;ReadPosRankSum=1.487;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,24:42:99:800,0,577
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1712 chr1 73823 . G C 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.881;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-0.311;QD=16.01;ReadPosRankSum=1.450;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,26:53:99:877,0,914
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1713 chr1 73849 . G A 1301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.816;DP=62;Dels=0.00;FS=1.017;HaplotypeScore=3.9989;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-0.015;QD=21.00;ReadPosRankSum=-0.146;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,39:62:99:1330,0,730
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1714 chr1 73870 . G A 1246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.344;DP=62;Dels=0.00;FS=3.539;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.230;QD=20.11;ReadPosRankSum=0.861;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,37:62:99:1275,0,847
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1715 chr1 73877 . A G 1141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.674;DP=64;Dels=0.00;FS=3.431;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=-0.836;QD=17.84;ReadPosRankSum=1.915;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,35:64:99:1170,0,987
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1716 chr1 73917 . A G 1108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.277;DP=66;Dels=0.00;FS=2.047;HaplotypeScore=1.9912;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=-0.905;QD=16.80;ReadPosRankSum=-0.686;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,34:66:99:1137,0,1083
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1717 chr1 73927 . T C 1021.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.691;DP=59;Dels=0.00;FS=3.614;HaplotypeScore=2.6984;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=0.812;QD=17.32;ReadPosRankSum=-1.419;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,31:59:99:1050,0,941
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1718 chr1 73941 . C G 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.144;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=2.6987;MLEAC=1;MLEAF=0.500;MQ=58.89;MQ0=0;MQRankSum=0.313;QD=14.74;ReadPosRankSum=0.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,25:55:99:839,0,1011
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1719 chr1 73956 . A C 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=45;Dels=0.00;FS=4.291;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-0.468;QD=13.53;ReadPosRankSum=0.514;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:637,0,849
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|
1720 chr1 74024 . G C 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.254;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.16;MQ0=3;MQRankSum=-2.569;QD=14.19;ReadPosRankSum=0.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,26:46:99:681,0,673
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1721 chr1 74047 . G A 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.369;DP=52;Dels=0.00;FS=6.153;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.43;MQ0=4;MQRankSum=-3.097;QD=12.90;ReadPosRankSum=-1.455;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,28:52:99:699,0,647
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1722 chr1 74080 . G A 629.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=58;Dels=0.00;FS=2.389;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=48.01;MQ0=4;MQRankSum=-5.098;QD=10.86;ReadPosRankSum=1.030;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:658,0,902
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|
1723 chr1 74086 . A T 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.258;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=50.43;MQ0=1;MQRankSum=-6.245;QD=9.29;ReadPosRankSum=1.114;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,26:54:99:530,0,995
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|
1724 chr1 74089 . T G 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=1;MQRankSum=-6.297;QD=9.30;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:540,0,1006
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|
|
1725 chr1 74105 . G A 433.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.603;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=50.74;MQ0=1;MQRankSum=-6.154;QD=8.18;ReadPosRankSum=-0.700;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:462,0,1044
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|
|
1726 chr1 74115 . A G 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.271;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=50.24;MQ0=1;MQRankSum=-5.772;QD=6.19;ReadPosRankSum=-0.920;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,21:47:99:319,0,952
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|
|
1727 chr1 74119 . A G 308.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.277;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=50.57;MQ0=1;MQRankSum=-5.551;QD=7.02;ReadPosRankSum=-0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,19:44:99:337,0,895
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|
|
1728 chr1 74274 . A T 879.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.47;MQ0=0;QD=29.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:908,69,0
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|
|
1729 chr1 74343 . C T 944.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.338;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=0.918;QD=17.18;ReadPosRankSum=3.291;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:973,0,882
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|
|
1730 chr1 74475 . C T 1026.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.652;DP=61;Dels=0.00;FS=12.530;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.79;MQ0=0;MQRankSum=-6.052;QD=16.83;ReadPosRankSum=2.532;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,30:61:99:1055,0,1074
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|
|
1731 chr1 74477 . T C 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.511;DP=59;Dels=0.00;FS=10.241;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=-5.936;QD=17.84;ReadPosRankSum=2.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1081,0,1017
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|
|
1732 chr1 74481 . G A 1104.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.304;DP=60;Dels=0.00;FS=7.540;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.70;MQ0=0;MQRankSum=-5.682;QD=18.41;ReadPosRankSum=1.030;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,32:60:99:1133,0,933
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|
|
1733 chr1 74490 . A G 836.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.635;DP=62;Dels=0.00;FS=5.488;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.78;MQ0=0;MQRankSum=5.728;QD=13.50;ReadPosRankSum=1.106;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:36,26:62:99:865,0,1275
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|
|
1734 chr1 74532 . C T 1134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.207;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=0;MQRankSum=-1.874;QD=18.60;ReadPosRankSum=-1.368;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1163,0,974
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|
|
1735 chr1 74539 . T A 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.904;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-2.447;QD=15.63;ReadPosRankSum=0.686;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:935,0,1102
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|
|
1736 chr1 74540 . A T 901.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.171;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.639;QD=15.55;ReadPosRankSum=0.733;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:930,0,1112
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|
|
1737 chr1 74544 . T C 1012.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.120;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=1.937;QD=16.08;ReadPosRankSum=0.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,30:63:99:1041,0,1120
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|
|
1738 chr1 74554 . T C 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.591;DP=62;Dels=0.00;FS=0.939;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=1.760;QD=15.63;ReadPosRankSum=1.056;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,31:62:99:997,0,1066
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|
|
1739 chr1 74559 . A G 961.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.648;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.806;QD=16.03;ReadPosRankSum=1.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,30:60:99:990,0,1042
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|
|
1740 chr1 74590 . G A 779.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.100;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=2.9966;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=0.903;QD=14.71;ReadPosRankSum=2.690;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,23:53:99:808,0,980
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|
|
1741 chr1 74638 . C T 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.820;DP=55;Dels=0.00;FS=1.026;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.49;MQ0=0;MQRankSum=1.355;QD=14.74;ReadPosRankSum=-1.574;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:839,0,868
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|
|
1742 chr1 74648 . C A 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.491;DP=53;Dels=0.00;FS=3.775;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=1.331;QD=14.88;ReadPosRankSum=-1.153;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:817,0,917
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|
1743 chr1 74652 . T C 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.459;DP=50;Dels=0.00;FS=1.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.23;MQ0=0;MQRankSum=1.026;QD=14.20;ReadPosRankSum=-1.085;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:738,0,887
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|
1744 chr1 74691 . C T 1222.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.25;MQ0=0;QD=28.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,34:34:96:1251,96,0
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1745 chr1 74732 . C A 514.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.435;DP=42;Dels=0.00;FS=18.002;HaplotypeScore=1.7219;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-0.102;QD=12.26;ReadPosRankSum=-0.615;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:543,0,832
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|
1746 chr1 74805 . G A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.142;DP=32;Dels=0.00;FS=11.588;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.183;QD=8.59;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:303,0,769
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|
1747 chr1 74809 . A G 198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.788;DP=28;Dels=0.00;FS=11.253;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=1.297;QD=7.10;ReadPosRankSum=0.432;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,8:28:99:227,0,624
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|
1748 chr1 74810 . C T 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.348;DP=28;Dels=0.00;FS=11.253;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-0.687;QD=7.67;ReadPosRankSum=0.280;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,8:28:99:243,0,706
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|
1749 chr1 74816 . A T 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.472;DP=30;Dels=0.00;FS=8.475;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=2.064;QD=5.89;ReadPosRankSum=-0.025;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,7:30:99:205,0,702
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|
1750 chr1 74826 . T A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.501;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=19.9448;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=0.122;QD=28.38;ReadPosRankSum=2.717;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:4,19:23:88:681,0,88
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|
1751 chr1 74830 . A T 738.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.315;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=17.9789;MLEAC=2;MLEAF=1.00;MQ=59.00;MQ0=0;MQRankSum=1.419;QD=33.58;ReadPosRankSum=0.315;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:1,21:22:25:767,25,0
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|
1752 chr1 74836 . A T 949.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=18.7128;MLEAC=2;MLEAF=1.00;MQ=59.12;MQ0=0;QD=28.63;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,25:25:75:978,75,0
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1753 chr1 74877 . C T 1344.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.09;MQ0=0;QD=29.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1373,105,0
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|
1754 chr1 74921 . A G 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.720;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=0;MQRankSum=-0.573;QD=6.31;ReadPosRankSum=1.929;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:249,0,790
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|
1755 chr1 75391 . G T 704.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.040;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=3.7544;MLEAC=2;MLEAF=1.00;MQ=48.50;MQ0=0;MQRankSum=-0.901;QD=28.19;ReadPosRankSum=1.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:1,24:25:25:733,25,0
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|
1756 chr1 75393 . T C 692.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.069;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=2.9658;MLEAC=2;MLEAF=1.00;MQ=48.50;MQ0=0;MQRankSum=-1.040;QD=27.71;ReadPosRankSum=1.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:1,24:25:24:721,24,0
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|
1757 chr1 75399 . C A 731.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.96;MQ0=0;QD=30.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,24:24:60:760,60,0
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1758 chr1 75407 . G A 466.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.02;MQ0=0;QD=27.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,17:17:39:495,39,0
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1759 chr1 75408 . T C 474.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.02;MQ0=0;QD=27.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,17:17:39:503,39,0
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1760 chr1 75441 . A G 77.28 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.70;MQ0=0;QD=19.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,4:4:9:105,9,0
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|
1761 chr1 75443 . A G 77.28 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.70;MQ0=0;QD=19.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,4:4:9:105,9,0
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|
1762 chr1 75447 . C T 75.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.27;MQ0=0;QD=25.09;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:103,9,0
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|
1763 chr1 75675 . G T 46.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:74,6,0
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|
1764 chr1 75678 . G T 88.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:116,9,0
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|
1765 chr1 75695 . T C 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.207;DP=34;Dels=0.00;FS=1.377;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.62;MQ0=1;MQRankSum=-0.738;QD=15.23;ReadPosRankSum=0.018;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:546,0,545
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|
1766 chr1 75719 . C T 1840.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.36;MQ0=1;QD=26.81;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1869,138,0
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|
|
1767 chr1 75727 . A G 2171.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.64;MQ0=0;QD=34.26;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2200,163,0
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|
|
1768 chr1 75762 . C T 764.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.300;DP=56;Dels=0.00;FS=11.912;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.737;QD=13.66;ReadPosRankSum=-0.886;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:793,0,1062
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|
|
1769 chr1 75763 . T C 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.640;DP=55;Dels=0.00;FS=9.903;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.486;QD=13.21;ReadPosRankSum=-0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:755,0,1074
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|
1770 chr1 75764 . A G 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.339;DP=55;Dels=0.00;FS=9.903;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=0.930;QD=13.14;ReadPosRankSum=-0.930;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:751,0,1072
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|
1771 chr1 75807 . A C 597.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.697;DP=47;Dels=0.00;FS=1.116;HaplotypeScore=3.2018;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=0;MQRankSum=-0.075;QD=12.72;ReadPosRankSum=-0.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:626,0,814
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|
1772 chr1 75832 . A G 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.198;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=13.9498;MLEAC=1;MLEAF=0.500;MQ=54.71;MQ0=0;MQRankSum=-3.243;QD=6.99;ReadPosRankSum=3.243;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,7:22:99:182,0,490
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|
1773 chr1 75838 . A C,T 525.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=11.9502;MLEAC=1,1;MLEAF=0.500,0.500;MQ=53.83;MQ0=0;QD=27.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/2:0,7,12:19:99:664,409,388,255,0,222
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1774 chr1 75850 . G T 453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.661;DP=23;Dels=0.00;FS=4.400;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-1.228;QD=19.73;ReadPosRankSum=0.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:9,14:23:99:482,0,253
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|
1775 chr1 75905 . T G 911.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.627;DP=45;Dels=0.00;FS=4.849;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=1;MQRankSum=-0.699;QD=20.26;ReadPosRankSum=-0.337;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,27:45:99:940,0,570
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1776 chr1 75930 . T C 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;DP=54;Dels=0.00;FS=8.156;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=1;MQRankSum=-2.270;QD=12.68;ReadPosRankSum=-0.996;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,24:54:99:713,0,1060
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1777 chr1 75970 . C G 1604.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.17;MQ0=1;QD=31.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1633,120,0
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1778 chr1 76013 . T G 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.758;DP=38;Dels=0.00;FS=1.402;HaplotypeScore=1.9956;MLEAC=1;MLEAF=0.500;MQ=55.23;MQ0=1;MQRankSum=0.479;QD=12.73;ReadPosRankSum=-1.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:512,0,658
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|
1779 chr1 76032 . A T 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.051;DP=43;Dels=0.00;FS=5.229;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.57;MQ0=1;MQRankSum=1.973;QD=12.72;ReadPosRankSum=-0.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:575,0,722
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1780 chr1 76087 . C A 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.047;DP=51;Dels=0.00;FS=11.471;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=57.19;MQ0=0;MQRankSum=1.732;QD=14.84;ReadPosRankSum=0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:785,0,818
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1781 chr1 76168 . T C 841.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.282;DP=43;Dels=0.00;FS=2.727;HaplotypeScore=5.8324;MLEAC=1;MLEAF=0.500;MQ=56.98;MQ0=1;MQRankSum=-0.743;QD=19.58;ReadPosRankSum=2.024;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,26:43:99:870,0,570
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1782 chr1 76236 . C A 728.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=13.5311;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:757,57,0
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1783 chr1 76283 . C A 1892.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.84;MQ0=0;QD=28.55;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1921,147,0
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1784 chr1 76328 . C T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.666;DP=51;Dels=0.00;FS=4.307;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.62;MQ0=0;MQRankSum=-0.205;QD=10.86;ReadPosRankSum=-2.893;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,19:51:99:582,0,977
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1785 chr1 76334 . A G 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.425;DP=45;Dels=0.00;FS=1.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=2.653;QD=12.17;ReadPosRankSum=-1.587;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,18:45:99:576,0,815
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1786 chr1 76427 . A C 759.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.347;DP=54;Dels=0.00;FS=12.969;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=1;MQRankSum=-0.169;QD=14.07;ReadPosRankSum=0.508;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,26:54:99:788,0,919
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1787 chr1 76443 . T C 879.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.715;DP=59;Dels=0.00;FS=11.873;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=1;MQRankSum=0.451;QD=14.91;ReadPosRankSum=-0.513;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:908,0,963
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1788 chr1 76465 . C T 822.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.671;DP=50;Dels=0.00;FS=19.919;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=1;MQRankSum=-1.733;QD=16.46;ReadPosRankSum=-0.711;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,27:50:99:851,0,769
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1789 chr1 76478 . G T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.821;DP=48;Dels=0.00;FS=13.782;HaplotypeScore=145.9761;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=1;MQRankSum=-2.207;QD=15.77;ReadPosRankSum=0.565;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:785,0,657
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1790 chr1 76500 . G T 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.996;DP=35;Dels=0.00;FS=1.972;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=0.959;QD=0.57;ReadPosRankSum=-3.137;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,4:35:48:48,0,1103
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1791 chr1 76506 . T G 1303.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.25;MQ0=0;QD=30.53;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1332,99,0
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1792 chr1 76543 . A C,T 956.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=1.625;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=9.9300;MLEAC=1,1;MLEAF=0.500,0.500;MQ=55.99;MQ0=0;MQRankSum=0.542;QD=29.88;ReadPosRankSum=0.650;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/2:1,12,19:32:99:1134,701,665,433,0,376
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1793 chr1 76552 . C A 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.464;DP=33;Dels=0.00;FS=1.376;HaplotypeScore=16.6986;MLEAC=1;MLEAF=0.500;MQ=55.88;MQ0=0;MQRankSum=-3.019;QD=17.72;ReadPosRankSum=0.524;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,18:33:99:613,0,416
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1794 chr1 76554 . A T 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.103;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=14.9106;MLEAC=1;MLEAF=0.500;MQ=55.91;MQ0=0;MQRankSum=-2.480;QD=15.93;ReadPosRankSum=0.827;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:570,0,574
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1795 chr1 76667 . C A 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=50;Dels=0.00;FS=2.539;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.616;QD=22.38;ReadPosRankSum=2.961;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,32:50:99:1147,0,573
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1796 chr1 76736 . T C 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.314;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=2.2657;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.771;QD=21.09;ReadPosRankSum=-0.603;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,27:44:99:956,0,527
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1797 chr1 76758 . A G 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.695;DP=38;Dels=0.00;FS=1.289;HaplotypeScore=16.4637;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.370;QD=19.39;ReadPosRankSum=0.103;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,22:38:99:765,0,537
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1798 chr1 76765 . A T 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.716;DP=38;Dels=0.00;FS=1.281;HaplotypeScore=62.8561;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=0.219;QD=17.55;ReadPosRankSum=1.535;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,20:38:99:695,0,601
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1799 chr1 76784 . G A 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.023;DP=44;Dels=0.00;FS=2.498;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.258;QD=14.59;ReadPosRankSum=-1.433;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:670,0,738
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1800 chr1 76813 . G T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.627;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=1.777;QD=19.61;ReadPosRankSum=-1.476;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,32:52:99:1048,0,649
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1801 chr1 76827 . C T 996.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.020;DP=50;Dels=0.00;FS=1.117;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=-1.020;QD=19.94;ReadPosRankSum=-1.218;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,30:50:99:1025,0,663
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1802 chr1 76831 . G A 1076.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=-0.124;QD=19.94;ReadPosRankSum=-1.136;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,33:54:99:1105,0,628
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1803 chr1 76885 . G C 1078.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.785;DP=51;Dels=0.00;FS=8.452;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.280;QD=21.15;ReadPosRankSum=0.878;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1107,0,632
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1804 chr1 76963 . A G 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.690;DP=35;Dels=0.00;FS=1.313;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.421;QD=19.62;ReadPosRankSum=0.589;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V46A|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:14,21:35:99:715,0,396
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1805 chr1 76964 . C A 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.051;DP=35;Dels=0.00;FS=1.313;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.364;QD=19.68;ReadPosRankSum=0.791;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V46L|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:14,21:35:99:717,0,439
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1806 chr1 76995 . T C 912.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.55;MQ0=0;QD=34.12;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A35|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,24:24:72:941,72,0
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1807 chr1 77019 . T G 807.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=59.25;MQ0=0;QD=28.76;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G27|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,22:22:66:836,66,0
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1808 chr1 77028 . G T 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.083;QD=11.11;ReadPosRankSum=-0.305;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agA|S24R|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:15,10:25:99:306,0,525
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1809 chr1 77030 . T C 1001.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=59.78;MQ0=0;QD=33.45;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S24G|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,26:26:78:1030,78,0
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1810 chr1 77036 . C G 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.023;DP=29;Dels=0.00;FS=2.741;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.482;QD=9.75;ReadPosRankSum=1.399;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ctc|V22L|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,10:29:99:311,0,667
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1811 chr1 77040 . A C 1106.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=0;QD=28.97;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atT/atG|I20M|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,31:31:87:1135,87,0
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1812 chr1 77066 . C T 605.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=38;Dels=0.00;FS=5.701;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-1.686;QD=15.94;ReadPosRankSum=2.051;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A12T|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:18,19:38:99:634,0,588
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1813 chr1 77068 . A G 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.949;DP=38;Dels=0.00;FS=5.701;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-2.131;QD=16.28;ReadPosRankSum=2.336;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V11A|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,19:38:99:647,0,593
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1814 chr1 77072 . G C 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.606;DP=38;Dels=0.00;FS=5.701;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-1.518;QD=15.65;ReadPosRankSum=2.628;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L10V|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,19:38:99:623,0,636
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1815 chr1 77092 . C G 1448.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=2.9948;MLEAC=2;MLEAF=1.00;MQ=58.31;MQ0=0;QD=33.69;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gCg|G3A|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,42:43:99:1477,111,0
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1816 chr1 77096 . C T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.577;DP=45;Dels=0.00;FS=6.823;HaplotypeScore=2.9948;MLEAC=1;MLEAF=0.500;MQ=58.12;MQ0=0;MQRankSum=-1.215;QD=17.06;ReadPosRankSum=0.534;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E2K|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:22,23:45:99:796,0,679
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1817 chr1 77106 . T C 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.785;DP=45;Dels=0.00;FS=4.485;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.12;MQ0=0;MQRankSum=-1.035;QD=17.26;ReadPosRankSum=-1.240;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:21,24:45:99:805,0,662
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1818 chr1 77122 . A G 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.595;DP=34;Dels=0.00;FS=3.155;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=0;MQRankSum=-1.700;QD=14.32;ReadPosRankSum=-0.728;EFF=START_GAINED(LOW||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,15:34:99:515,0,632
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1819 chr1 77126 . A T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.204;DP=37;Dels=0.00;FS=7.143;HaplotypeScore=3.7335;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=-1.844;QD=14.97;ReadPosRankSum=-0.808;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:20,17:37:99:582,0,647
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1820 chr1 77144 . A C 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.300;DP=41;Dels=0.00;FS=4.506;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=-1.265;QD=15.85;ReadPosRankSum=0.170;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:21,20:41:99:678,0,682
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1821 chr1 77180 . C A 701.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.879;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=4.1179;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.179;QD=17.54;ReadPosRankSum=-0.594;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:16,24:40:99:730,0,535
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1822 chr1 77221 . C G 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.565;DP=43;Dels=0.00;FS=14.813;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.319;QD=20.88;ReadPosRankSum=-0.163;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,27:43:99:926,0,502
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1823 chr1 77244 . G C 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=39;Dels=0.00;FS=5.550;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.512;QD=21.81;ReadPosRankSum=0.454;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:14,25:39:99:879,0,425
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1824 chr1 77298 . T G 809.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.048;DP=35;Dels=0.00;FS=5.506;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-1.901;QD=23.14;ReadPosRankSum=1.190;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,24:35:99:838,0,318
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1825 chr1 77325 . T A 1222.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=55.78;MQ0=0;QD=37.76;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1251,96,0
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1826 chr1 77332 . G A 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.198;DP=32;Dels=0.00;FS=3.329;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=-0.516;QD=22.34;ReadPosRankSum=0.278;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,21:32:99:743,0,352
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1827 chr1 77376 . T C 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.170;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=83.6545;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=-2.434;QD=15.40;ReadPosRankSum=0.431;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:783,0,747
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1828 chr1 77378 . A C 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.290;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=124.2479;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=-2.053;QD=15.32;ReadPosRankSum=0.431;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:779,0,892
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1829 chr1 77438 . C T 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.363;DP=53;Dels=0.00;FS=15.115;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-0.633;QD=16.94;ReadPosRankSum=-2.539;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:926,0,869
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1830 chr1 77442 . T G 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.884;DP=51;Dels=0.00;FS=15.703;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.218;QD=15.02;ReadPosRankSum=3.474;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:794,0,934
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1831 chr1 77449 . T C 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.432;DP=48;Dels=0.00;FS=11.196;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.972;QD=13.39;ReadPosRankSum=2.206;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,20:48:99:671,0,945
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1832 chr1 77450 . A G 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.917;DP=46;Dels=0.00;FS=11.459;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=0.853;QD=14.34;ReadPosRankSum=1.673;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,20:46:99:688,0,862
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1833 chr1 77458 . A T 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.272;DP=51;Dels=0.00;FS=16.807;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=1;MQRankSum=2.301;QD=15.23;ReadPosRankSum=0.146;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:805,0,791
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1834 chr1 77464 . G A 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.681;DP=49;Dels=0.00;FS=17.115;HaplotypeScore=1.6281;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=1;MQRankSum=-0.908;QD=16.95;ReadPosRankSum=-1.610;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:859,0,697
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1835 chr1 77489 . G A 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.648;DP=46;Dels=0.00;FS=12.506;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=57.16;MQ0=2;MQRankSum=-0.625;QD=14.45;ReadPosRankSum=2.345;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:693,0,690
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1836 chr1 77491 . A G 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.194;DP=45;Dels=0.00;FS=15.152;HaplotypeScore=1.9545;MLEAC=1;MLEAF=0.500;MQ=56.71;MQ0=2;MQRankSum=2.203;QD=12.71;ReadPosRankSum=-1.489;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,19:45:99:600,0,730
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1837 chr1 77495 . A G 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.505;DP=41;Dels=0.00;FS=16.483;HaplotypeScore=1.9545;MLEAC=1;MLEAF=0.500;MQ=56.38;MQ0=2;MQRankSum=2.237;QD=11.36;ReadPosRankSum=-0.476;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:494,0,766
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1838 chr1 77531 . A G 760.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.516;DP=49;Dels=0.00;FS=11.272;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=3;MQRankSum=4.899;QD=15.53;ReadPosRankSum=1.626;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:789,0,677
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1839 chr1 77535 . C T 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=49;Dels=0.00;FS=13.395;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=3;MQRankSum=-5.229;QD=14.63;ReadPosRankSum=-2.065;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:745,0,801
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1840 chr1 77544 . C T 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.557;DP=48;Dels=0.00;FS=11.235;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.09;MQ0=3;MQRankSum=-5.517;QD=13.20;ReadPosRankSum=-0.330;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,22:48:99:662,0,770
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1841 chr1 77549 . C G 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.738;DP=50;Dels=0.00;FS=10.772;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.34;MQ0=3;MQRankSum=-5.596;QD=12.14;ReadPosRankSum=0.332;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:635,0,869
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1842 chr1 77557 . A G 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.869;DP=45;Dels=0.00;FS=9.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=3;MQRankSum=-5.553;QD=14.15;ReadPosRankSum=0.416;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:665,0,732
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1843 chr1 77577 . T G 261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.195;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.12;MQ0=3;MQRankSum=-3.998;QD=6.89;ReadPosRankSum=2.292;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,12:38:99:290,0,880
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1844 chr1 77581 . T G 1321.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=55.74;MQ0=2;QD=31.22;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1350,99,0
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1845 chr1 77582 . A G 1318.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=55.61;MQ0=2;QD=29.89;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1347,99,0
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1846 chr1 77589 . C T 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.438;DP=42;Dels=0.00;FS=4.743;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=2;MQRankSum=-2.271;QD=11.95;ReadPosRankSum=-0.055;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:530,0,807
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1847 chr1 77592 . G A 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.734;DP=43;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=2;MQRankSum=2.439;QD=16.46;ReadPosRankSum=0.952;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:736,0,657
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1848 chr1 77593 . T C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.535;DP=43;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=2;MQRankSum=-1.969;QD=15.04;ReadPosRankSum=-0.874;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:675,0,722
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1849 chr1 77615 . C T 710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.765;DP=43;Dels=0.00;FS=2.820;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.50;MQ0=2;MQRankSum=-0.327;QD=16.53;ReadPosRankSum=-0.327;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:739,0,655
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1850 chr1 77617 . C T 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.975;DP=42;Dels=0.00;FS=4.575;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.58;MQ0=2;MQRankSum=0.488;QD=16.40;ReadPosRankSum=0.027;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,22:42:99:717,0,653
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1851 chr1 77620 . T C 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.342;DP=43;Dels=0.00;FS=2.687;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=2;MQRankSum=0.013;QD=12.79;ReadPosRankSum=0.781;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,17:43:99:578,0,822
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1852 chr1 77633 . G A 475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.964;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=1;MQRankSum=1.015;QD=11.33;ReadPosRankSum=-0.555;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:504,0,850
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1853 chr1 77648 . C T 387.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.970;DP=44;Dels=0.00;FS=1.269;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=1;MQRankSum=0.304;QD=8.81;ReadPosRankSum=-0.569;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:416,0,909
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1854 chr1 77650 . T C 1540.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=2;MLEAF=1.00;MQ=58.05;MQ0=1;QD=31.92;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1569,120,0
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1855 chr1 77695 . A G 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.171;DP=48;Dels=0.00;FS=11.450;HaplotypeScore=1.9984;MLEAC=1;MLEAF=0.500;MQ=56.59;MQ0=1;MQRankSum=-1.215;QD=11.39;ReadPosRankSum=-2.156;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,19:48:99:575,0,980
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1856 chr1 77770 . C T 2115.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.00;MQ0=2;QD=26.51;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2144,163,0
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1857 chr1 77798 . A G 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.110;DP=51;Dels=0.00;FS=4.291;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.36;MQ0=1;MQRankSum=-0.292;QD=13.56;ReadPosRankSum=-0.856;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:720,0,928
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|
|
1858 chr1 77814 . G T 954.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.710;DP=51;Dels=0.00;FS=4.322;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=54.03;MQ0=1;MQRankSum=-1.124;QD=18.72;ReadPosRankSum=0.283;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,29:51:99:983,0,686
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|
|
1859 chr1 77873 . G A 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.393;DP=45;Dels=0.00;FS=1.232;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=1.065;QD=20.19;ReadPosRankSum=-2.142;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,28:45:99:937,0,508
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|
|
1860 chr1 77951 . C A 2019.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=2.7336;MLEAC=2;MLEAF=1.00;MQ=59.41;MQ0=0;QD=31.25;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2048,159,0
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|
|
1861 chr1 77986 . T C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.287;DP=56;Dels=0.00;FS=5.494;HaplotypeScore=1.9774;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=-1.712;QD=14.80;ReadPosRankSum=0.778;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,28:56:99:857,0,933
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|
|
1862 chr1 78007 . C T 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.299;DP=43;Dels=0.00;FS=1.315;HaplotypeScore=19.9836;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=0.842;QD=11.18;ReadPosRankSum=0.565;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,16:43:99:509,0,882
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|
|
1863 chr1 78009 . C T 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.704;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=21.9828;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-1.014;QD=19.65;ReadPosRankSum=-0.060;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,26:44:99:893,0,579
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|
|
1864 chr1 78012 . T A 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.563;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=21.9828;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.037;QD=18.65;ReadPosRankSum=-0.185;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:830,0,589
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|
|
1865 chr1 78019 . T C 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.817;DP=44;Dels=0.00;FS=3.112;HaplotypeScore=24.9845;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-0.446;QD=10.13;ReadPosRankSum=2.105;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,15:44:99:474,0,1015
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|
|
1866 chr1 78027 . T C 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.359;DP=44;Dels=0.00;FS=12.758;HaplotypeScore=6.9973;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.701;QD=1.72;ReadPosRankSum=-1.043;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:38,6:44:99:104,0,1372
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|
1867 chr1 78118 . T A 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.504;DP=54;Dels=0.00;FS=1.040;HaplotypeScore=35.7719;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-0.892;QD=19.46;ReadPosRankSum=1.994;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,31:54:99:1079,0,770
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|
|
1868 chr1 78134 . C T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.779;DP=54;Dels=0.00;FS=2.393;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=0.099;QD=11.72;ReadPosRankSum=-0.958;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:34,20:54:99:661,0,1176
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1869 chr1 78240 . T C 1102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.525;DP=57;Dels=0.00;FS=3.838;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=0.234;QD=19.35;ReadPosRankSum=0.444;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1131,0,782
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|
1870 chr1 78243 . T A 1121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.267;DP=58;Dels=0.00;FS=5.380;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=0.361;QD=19.34;ReadPosRankSum=0.848;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1150,0,823
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1871 chr1 78259 . A G 988.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.319;DP=58;Dels=0.00;FS=5.430;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=1.330;QD=17.05;ReadPosRankSum=0.319;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1017,0,977
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|
1872 chr1 78296 . C T 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.195;DP=35;Dels=0.00;FS=5.073;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.286;QD=20.34;ReadPosRankSum=1.667;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,21:35:99:740,0,458
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1873 chr1 78417 . A G 2257.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.25;MQ0=1;QD=27.55;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2286,172,0
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|
1874 chr1 78420 . T C 2412.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.30;MQ0=1;QD=32.78;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,63:63:99:2441,184,0
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|
1875 chr1 78459 . A G 1049.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.567;DP=56;Dels=0.00;FS=1.071;HaplotypeScore=2.7605;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=4;MQRankSum=1.156;QD=18.75;ReadPosRankSum=1.026;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,33:56:99:1078,0,681
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|
1876 chr1 78480 . G T 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.047;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9932;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=4;MQRankSum=-1.866;QD=7.95;ReadPosRankSum=-1.529;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,17:49:99:418,0,1082
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1877 chr1 78503 . A C 1406.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.844;DP=60;Dels=0.00;FS=2.699;HaplotypeScore=42.4334;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=3;MQRankSum=1.437;QD=23.45;ReadPosRankSum=2.809;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,45:60:99:1435,0,403
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1878 chr1 78548 . T A 2170.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.19;MQ0=0;QD=24.73;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2199,166,0
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|
1879 chr1 78601 . G A 1151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.289;DP=48;Dels=0.00;FS=5.335;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.23;MQ0=0;MQRankSum=-0.133;QD=24.00;ReadPosRankSum=-0.200;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,33:48:99:1180,0,463
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1880 chr1 78639 . C A 1912.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.43;MQ0=0;QD=26.86;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1941,147,0
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|
1881 chr1 78753 . G T 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.473;DP=65;Dels=0.00;FS=0.960;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.007;QD=12.77;ReadPosRankSum=-0.353;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:38,27:65:99:858,0,1336
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1882 chr1 78787 . G A 1365.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.554;DP=61;Dels=0.00;FS=1.030;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.660;QD=22.39;ReadPosRankSum=-0.751;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,40:61:99:1394,0,614
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1883 chr1 78815 . A G 1168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.008;DP=57;Dels=0.00;FS=3.773;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.336;QD=20.50;ReadPosRankSum=1.320;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,35:57:99:1197,0,695
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1884 chr1 78892 . C T 925.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.979;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=2.5773;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.584;QD=15.69;ReadPosRankSum=0.175;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,28:59:99:954,0,1057
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1885 chr1 78931 . G A 1066.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.869;DP=63;Dels=0.00;FS=11.290;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.796;QD=16.93;ReadPosRankSum=-1.025;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,33:63:99:1095,0,1023
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1886 chr1 78981 . T C 131.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.954;DP=27;Dels=0.00;FS=12.207;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.904;QD=4.88;ReadPosRankSum=2.537;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,6:27:99:160,0,693
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1887 chr1 78994 . T A 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.138;DP=38;Dels=0.00;FS=22.047;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=2.492;QD=20.10;ReadPosRankSum=-0.738;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,25:38:99:792,0,376
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1888 chr1 79011 . A T 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.991;DP=42;Dels=0.00;FS=18.301;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=-0.654;QD=7.21;ReadPosRankSum=1.573;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,12:42:99:331,0,1024
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1889 chr1 79031 . C A 910.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=45;Dels=0.00;FS=23.835;HaplotypeScore=3.8993;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=2.704;QD=20.24;ReadPosRankSum=0.386;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,28:45:99:939,0,503
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1890 chr1 79032 . T C 1667.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.02;FS=0.000;HaplotypeScore=16.9978;MLEAC=2;MLEAF=1.00;MQ=59.30;MQ0=0;QD=32.21;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1696,126,0
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1891 chr1 79035 . C G 1664.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.115;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=3.8993;MLEAC=2;MLEAF=1.00;MQ=59.31;MQ0=0;MQRankSum=1.578;QD=32.37;ReadPosRankSum=0.654;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:1,44:45:92:1693,92,0
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1892 chr1 79092 . A C 405.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;DP=56;Dels=0.00;FS=20.015;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=59.96;MQ0=0;MQRankSum=-1.258;QD=7.25;ReadPosRankSum=1.147;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:41,15:56:99:434,0,1487
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1893 chr1 79155 . A G 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.851;DP=43;Dels=0.00;FS=24.229;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=-0.433;QD=4.20;ReadPosRankSum=1.776;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,9:43:99:209,0,1210
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1894 chr1 79179 . A G 1612.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.02;MQ0=0;QD=29.41;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1641,126,0
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1895 chr1 79211 . G A 279.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.436;DP=44;Dels=0.00;FS=24.701;HaplotypeScore=3.9990;MLEAC=1;MLEAF=0.500;MQ=55.60;MQ0=0;MQRankSum=-4.230;QD=6.36;ReadPosRankSum=2.095;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,12:44:99:308,0,1153
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1896 chr1 79215 . A G 268.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.314;DP=46;Dels=0.00;FS=28.108;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=55.80;MQ0=0;MQRankSum=-3.940;QD=5.84;ReadPosRankSum=2.539;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,12:46:99:297,0,1207
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1897 chr1 79219 . C T 269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.298;DP=48;Dels=0.00;FS=32.959;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=55.98;MQ0=0;MQRankSum=-4.417;QD=5.62;ReadPosRankSum=2.464;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:36,12:48:99:298,0,1293
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1898 chr1 79223 . A C 1751.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.7884;MLEAC=2;MLEAF=1.00;MQ=55.80;MQ0=0;QD=31.46;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1780,135,0
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1899 chr1 79242 . C T 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.484;DP=54;Dels=0.00;FS=36.287;HaplotypeScore=13.9681;MLEAC=1;MLEAF=0.500;MQ=54.78;MQ0=0;MQRankSum=-5.699;QD=8.00;ReadPosRankSum=-1.173;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:460,0,1314
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1900 chr1 79253 . C T 1141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.069;DP=49;Dels=0.00;FS=18.054;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.73;MQ0=0;MQRankSum=5.556;QD=23.30;ReadPosRankSum=2.594;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,32:49:99:1170,0,488
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1901 chr1 79258 . C T 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=50;Dels=0.00;FS=15.207;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.38;MQ0=0;MQRankSum=-4.996;QD=7.74;ReadPosRankSum=-1.397;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:415,0,1279
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1902 chr1 79284 . A T 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.956;DP=48;Dels=0.00;FS=2.747;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=-4.938;QD=8.83;ReadPosRankSum=1.401;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,15:48:99:452,0,1222
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1903 chr1 79288 . G C 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.423;DP=48;Dels=0.00;FS=2.747;HaplotypeScore=25.1292;MLEAC=1;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=-5.205;QD=8.68;ReadPosRankSum=1.690;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,15:48:99:445,0,1219
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1904 chr1 79300 . T A 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=-4.876;QD=8.74;ReadPosRankSum=1.877;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,14:44:99:413,0,1090
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1905 chr1 79321 . G C 581.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.836;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.16;MQ0=0;MQRankSum=-4.816;QD=15.72;ReadPosRankSum=-0.137;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:610,0,654
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1906 chr1 79322 . C A 1506.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.35;MQ0=0;QD=35.79;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1535,114,0
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1907 chr1 79337 . G A 466.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.043;DP=33;Dels=0.00;FS=3.093;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.87;MQ0=0;MQRankSum=-4.610;QD=14.14;ReadPosRankSum=1.392;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:495,0,617
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1908 chr1 79397 . C A 291.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.587;DP=32;Dels=0.00;FS=32.017;HaplotypeScore=1.9978;MLEAC=1;MLEAF=0.500;MQ=53.02;MQ0=0;MQRankSum=-4.602;QD=9.12;ReadPosRankSum=-2.420;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,11:32:99:320,0,754
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1909 chr1 79404 . T A 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.453;DP=40;Dels=0.00;FS=20.081;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-5.252;QD=10.74;ReadPosRankSum=-1.648;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:458,0,853
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1910 chr1 79408 . T A 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.460;DP=42;Dels=0.00;FS=18.695;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.17;MQ0=0;MQRankSum=-4.894;QD=11.90;ReadPosRankSum=-1.666;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:528,0,853
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1911 chr1 79425 . C T 435.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.446;DP=44;Dels=0.00;FS=12.871;HaplotypeScore=3.5215;MLEAC=1;MLEAF=0.500;MQ=56.34;MQ0=0;MQRankSum=-3.990;QD=9.90;ReadPosRankSum=1.522;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,15:44:99:464,0,918
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1912 chr1 79451 . G A 406.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.625;DP=45;Dels=0.00;FS=2.772;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-1.017;QD=9.04;ReadPosRankSum=1.361;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:435,0,1059
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1913 chr1 79452 . A T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.469;DP=46;Dels=0.00;FS=2.785;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=-1.218;QD=9.36;ReadPosRankSum=1.148;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:459,0,1031
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1914 chr1 79468 . C T 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=48;Dels=0.00;FS=1.129;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-0.623;QD=14.00;ReadPosRankSum=-0.748;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:700,0,913
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1915 chr1 79478 . G C 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.027;DP=53;Dels=0.00;FS=3.828;HaplotypeScore=1.6648;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.471;QD=16.94;ReadPosRankSum=-1.753;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,27:53:99:926,0,881
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1916 chr1 79598 . C T 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.841;DP=38;Dels=0.00;FS=9.653;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=0;MQRankSum=-3.061;QD=4.23;ReadPosRankSum=-0.877;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,8:38:99:189,0,1018
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1917 chr1 79615 . T C 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.118;DP=40;Dels=0.00;FS=4.786;HaplotypeScore=23.6444;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-5.315;QD=11.17;ReadPosRankSum=0.428;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,16:40:99:475,0,803
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1918 chr1 79617 . T A 190.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.588;DP=40;Dels=0.00;FS=9.975;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-4.200;QD=4.77;ReadPosRankSum=0.762;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,8:40:99:219,0,844
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1919 chr1 79618 . G A 138.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.167;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-3.364;QD=3.47;ReadPosRankSum=0.254;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,8:40:99:167,0,1124
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1920 chr1 79619 . C T 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.201;DP=40;Dels=0.00;FS=4.786;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-5.315;QD=11.09;ReadPosRankSum=1.256;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,16:40:99:472,0,808
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1921 chr1 79624 . C T 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.092;DP=37;Dels=0.00;FS=12.746;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-3.007;QD=4.86;ReadPosRankSum=1.605;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:208,0,974
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1922 chr1 79626 . G A 178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.125;DP=37;Dels=0.00;FS=13.178;HaplotypeScore=23.5003;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-3.007;QD=4.83;ReadPosRankSum=1.826;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:207,0,1010
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1923 chr1 79627 . A G 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.531;DP=37;Dels=0.00;FS=13.178;HaplotypeScore=23.5003;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-3.007;QD=4.86;ReadPosRankSum=1.900;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:208,0,1015
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1924 chr1 79640 . C T 478.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.230;DP=51;Dels=0.00;FS=14.590;HaplotypeScore=7.9961;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-1.369;QD=9.39;ReadPosRankSum=0.230;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,17:51:99:507,0,1160
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1925 chr1 79641 . G A 97.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.233;DP=51;Dels=0.00;FS=3.858;HaplotypeScore=7.9961;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-3.463;QD=1.92;ReadPosRankSum=3.189;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:44,7:51:99:126,0,1543
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1926 chr1 79670 . A G 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.536;DP=46;Dels=0.00;FS=2.588;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.55;MQ0=0;MQRankSum=-3.131;QD=14.97;ReadPosRankSum=1.235;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,21:46:99:717,0,801
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1927 chr1 79675 . C T 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.765;DP=43;Dels=0.00;FS=2.704;HaplotypeScore=18.9737;MLEAC=1;MLEAF=0.500;MQ=55.22;MQ0=0;MQRankSum=-2.223;QD=15.51;ReadPosRankSum=0.765;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:695,0,699
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1928 chr1 79697 . C A 978.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.94;MQ0=0;QD=24.70;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:1007,78,0
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1929 chr1 79745 . C G 1250.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.57;MQ0=0;QD=25.03;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,33:33:93:1279,93,0
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1930 chr1 79753 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.941;DP=37;Dels=0.00;FS=4.943;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=0.411;QD=13.21;ReadPosRankSum=0.290;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:517,0,675
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1931 chr1 79807 . C T 1019.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=7.7317;MLEAC=2;MLEAF=1.00;MQ=56.83;MQ0=0;QD=31.02;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,29:29:81:1048,81,0
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1932 chr1 79827 . C T 1289.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.78;MQ0=0;QD=35.57;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1318,99,0
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1933 chr1 79840 . A G 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.767;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-0.127;QD=12.11;ReadPosRankSum=0.055;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:428,0,660
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1934 chr1 79842 . G A 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.603;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=1.492;QD=20.75;ReadPosRankSum=-0.608;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,20:33:99:713,0,391
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1935 chr1 79860 . G A 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.431;DP=38;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-1.839;QD=14.44;ReadPosRankSum=0.000;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:577,0,643
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1936 chr1 80003 . A T 1616.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;QD=28.66;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1645,123,0
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1937 chr1 80017 . T A 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.877;DP=38;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=0.458;QD=12.63;ReadPosRankSum=0.340;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:508,0,721
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1938 chr1 80041 . T C 415.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.861;DP=37;Dels=0.00;FS=2.846;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.611;QD=11.24;ReadPosRankSum=-1.174;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:444,0,776
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1939 chr1 80045 . G C 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.955;DP=36;Dels=0.00;FS=1.366;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.811;QD=21.47;ReadPosRankSum=1.548;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,23:36:99:801,0,403
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1940 chr1 80079 . G C 459.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.802;DP=36;Dels=0.00;FS=4.943;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.481;QD=12.77;ReadPosRankSum=-2.952;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:488,0,737
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1941 chr1 80117 . C T 1871.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.15;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1900,141,0
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1942 chr1 80171 . A G 1589.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=19.9948;MLEAC=2;MLEAF=1.00;MQ=59.23;MQ0=0;QD=31.59;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1618,120,0
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1943 chr1 80184 . G A 817.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.229;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-2.084;QD=20.44;ReadPosRankSum=-1.173;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,24:40:99:846,0,495
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1944 chr1 80244 . T C 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.038;DP=32;Dels=0.00;FS=7.806;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.62;MQ0=0;MQRankSum=-3.927;QD=16.96;ReadPosRankSum=1.888;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,17:32:99:571,0,493
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1945 chr1 80416 . C A 796.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.16;MQ0=0;QD=33.46;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:825,63,0
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1946 chr1 80710 . A G 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.494;DP=36;Dels=0.00;FS=5.334;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=-1.350;QD=10.69;ReadPosRankSum=3.030;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,13:36:99:413,0,777
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1947 chr1 80861 . C T 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.300;DP=39;Dels=0.00;FS=2.826;HaplotypeScore=1.6649;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=0;MQRankSum=-1.328;QD=19.05;ReadPosRankSum=1.242;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,23:39:99:771,0,477
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1948 chr1 80867 . T C 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.071;DP=39;Dels=0.00;FS=2.869;HaplotypeScore=1.6649;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=0;MQRankSum=-1.827;QD=16.40;ReadPosRankSum=1.374;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,22:39:99:668,0,541
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1949 chr1 80925 . G C 316.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.311;DP=44;Dels=0.00;FS=22.159;HaplotypeScore=1.3670;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=1;MQRankSum=0.041;QD=7.20;ReadPosRankSum=0.203;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:345,0,1053
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1950 chr1 80926 . G A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.372;DP=43;Dels=0.00;FS=19.771;HaplotypeScore=1.3670;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=-0.744;QD=6.37;ReadPosRankSum=0.200;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,12:43:99:302,0,1088
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1951 chr1 80927 . G A 269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.143;DP=43;Dels=0.00;FS=19.771;HaplotypeScore=1.3670;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=0.057;QD=6.27;ReadPosRankSum=0.372;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,12:43:99:298,0,1101
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1952 chr1 80933 . T G 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.463;DP=45;Dels=0.00;FS=23.434;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=1;MQRankSum=-1.225;QD=7.17;ReadPosRankSum=0.856;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,13:45:99:351,0,1105
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1953 chr1 80959 . T A 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.398;DP=45;Dels=0.00;FS=5.002;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=1;MQRankSum=0.940;QD=10.44;ReadPosRankSum=-0.121;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,18:45:99:498,0,944
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1954 chr1 80967 . C T 496.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.143;DP=44;Dels=0.00;FS=5.002;HaplotypeScore=1.1567;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=1;MQRankSum=0.490;QD=11.29;ReadPosRankSum=0.666;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,17:44:99:525,0,924
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1955 chr1 81012 . C G 700.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.394;DP=40;Dels=0.00;FS=4.442;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.019;QD=17.52;ReadPosRankSum=1.672;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,22:40:99:729,0,588
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1956 chr1 81069 . C A 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.275;DP=44;Dels=0.00;FS=23.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.919;QD=12.97;ReadPosRankSum=0.155;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:599,0,905
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1957 chr1 81071 . T C 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.107;DP=44;Dels=0.00;FS=23.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.373;QD=12.54;ReadPosRankSum=0.060;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:580,0,911
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1958 chr1 81072 . C G 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.097;DP=45;Dels=0.00;FS=20.102;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.286;QD=12.66;ReadPosRankSum=-0.081;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,18:45:99:598,0,942
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1959 chr1 81095 . C G 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.970;DP=57;Dels=0.00;FS=23.054;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.781;QD=8.77;ReadPosRankSum=-1.073;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:39,18:57:99:528,0,1396
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1960 chr1 81130 . T G 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.398;DP=46;Dels=0.00;FS=1.253;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=-0.726;QD=8.95;ReadPosRankSum=0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:440,0,1117
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1961 chr1 81131 . T C 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.148;DP=46;Dels=0.00;FS=1.253;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=-1.523;QD=8.78;ReadPosRankSum=0.422;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:432,0,1127
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1962 chr1 81133 . T C 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.253;DP=45;Dels=0.00;FS=1.237;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=-0.951;QD=9.33;ReadPosRankSum=0.349;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,15:45:99:448,0,1081
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1963 chr1 81169 . A G 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.374;DP=49;Dels=0.00;FS=8.418;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-2.172;QD=13.10;ReadPosRankSum=2.091;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:670,0,987
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1964 chr1 81178 . C A 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.881;DP=50;Dels=0.00;FS=8.297;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.71;MQ0=0;MQRankSum=-3.555;QD=11.28;ReadPosRankSum=1.634;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:592,0,991
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1965 chr1 81185 . G A 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.606;DP=41;Dels=0.00;FS=12.377;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.19;MQ0=0;MQRankSum=-3.568;QD=11.26;ReadPosRankSum=1.403;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:490,0,818
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1966 chr1 81268 . T C 1503.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.94;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1532,114,0
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1967 chr1 81303 . C T 1678.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.39;MQ0=0;QD=31.18;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1707,126,0
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1968 chr1 81317 . C T 1738.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=1.3990;MLEAC=2;MLEAF=1.00;MQ=59.35;MQ0=0;QD=33.51;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1767,132,0
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1969 chr1 81331 . A C 1662.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=2.3989;MLEAC=2;MLEAF=1.00;MQ=59.33;MQ0=0;QD=37.65;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1691,129,0
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1970 chr1 81371 . G A 316.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.908;DP=48;Dels=0.00;FS=4.645;HaplotypeScore=1.9957;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=0;MQRankSum=-4.473;QD=6.60;ReadPosRankSum=-2.001;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,16:48:99:345,0,1127
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1971 chr1 81408 . A G 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.584;DP=53;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.12;MQ0=0;MQRankSum=-4.943;QD=8.94;ReadPosRankSum=2.754;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,19:53:99:502,0,1182
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1972 chr1 81418 . C T 463.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.718;DP=50;Dels=0.00;FS=21.604;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.53;MQ0=0;MQRankSum=-4.962;QD=9.28;ReadPosRankSum=2.375;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,18:50:99:492,0,1136
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1973 chr1 81422 . A T 1037.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.035;DP=48;Dels=0.00;FS=21.618;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.46;MQ0=0;MQRankSum=5.281;QD=21.62;ReadPosRankSum=-2.242;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,31:48:99:1066,0,457
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1974 chr1 81453 . C A 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.800;DP=46;Dels=0.00;FS=16.375;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=-4.476;QD=8.15;ReadPosRankSum=0.442;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:403,0,1150
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1975 chr1 81455 . G A 369.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.036;DP=46;Dels=0.00;FS=16.375;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=-3.808;QD=8.04;ReadPosRankSum=0.251;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:398,0,1139
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1976 chr1 81456 . C T 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.245;DP=47;Dels=0.00;FS=15.915;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.40;MQ0=0;MQRankSum=-4.013;QD=8.02;ReadPosRankSum=0.384;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,14:47:99:405,0,1154
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1977 chr1 81457 . G A 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.062;DP=46;Dels=0.00;FS=15.915;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=56.32;MQ0=0;MQRankSum=-3.617;QD=8.36;ReadPosRankSum=0.131;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:413,0,1151
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1978 chr1 81482 . G T 1236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.464;DP=50;Dels=0.00;FS=4.620;HaplotypeScore=1.7206;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=0;MQRankSum=2.035;QD=24.74;ReadPosRankSum=0.265;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,37:50:99:1265,0,325
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1979 chr1 81533 . A G 1828.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.609;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.61;MQ0=0;MQRankSum=2.352;QD=28.88;ReadPosRankSum=-0.619;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:2,48:50:99:1857,123,0
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1980 chr1 81544 . A G 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.466;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=2.8400;MLEAC=1;MLEAF=0.500;MQ=56.30;MQ0=0;MQRankSum=2.542;QD=8.41;ReadPosRankSum=-0.370;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:415,0,1040
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1981 chr1 81580 . A G 627.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.548;DP=43;Dels=0.00;FS=2.885;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=1.644;QD=14.60;ReadPosRankSum=-2.471;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:656,0,776
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1982 chr1 81581 . G A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.158;DP=43;Dels=0.00;FS=4.524;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=0.767;QD=15.18;ReadPosRankSum=-2.496;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:681,0,762
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1983 chr1 81594 . G A 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.680;DP=41;Dels=0.00;FS=1.230;HaplotypeScore=4.9968;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=0;MQRankSum=-0.251;QD=19.53;ReadPosRankSum=1.919;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,24:41:99:829,0,565
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1984 chr1 81600 . T G 715.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.903;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=4.9968;MLEAC=1;MLEAF=0.500;MQ=56.66;MQ0=0;MQRankSum=-2.660;QD=16.65;ReadPosRankSum=2.588;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:744,0,706
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1985 chr1 81603 . C G,T 1331.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=1.491;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.66;MQ0=0;MQRankSum=-0.443;QD=30.96;ReadPosRankSum=1.249;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/2:1,19,23:43:99:1506,809,783,668,0,633
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1986 chr1 81634 . A G 2035.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.31;MQ0=0;QD=30.65;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:2064,154,0
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1987 chr1 81638 . C T 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.276;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.96;MQ0=0;MQRankSum=-2.108;QD=15.37;ReadPosRankSum=-1.219;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,26:53:99:843,0,879
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1988 chr1 81650 . C T 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.645;DP=59;Dels=0.00;FS=0.989;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=51.91;MQ0=0;MQRankSum=1.677;QD=16.42;ReadPosRankSum=0.600;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,31:59:99:997,0,893
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1989 chr1 81655 . A T 817.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.767;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=50.82;MQ0=1;MQRankSum=-1.189;QD=14.60;ReadPosRankSum=-0.497;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:846,0,959
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1990 chr1 81660 . C G 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.667;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=50.26;MQ0=1;MQRankSum=-1.272;QD=14.65;ReadPosRankSum=-0.667;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:834,0,917
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1991 chr1 81676 . T A 1209.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.535;DP=37;Dels=0.03;FS=3.136;HaplotypeScore=2.9325;MLEAC=2;MLEAF=1.00;MQ=45.14;MQ0=1;MQRankSum=-1.733;QD=32.70;ReadPosRankSum=1.634;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:1,35:36:65:1238,65,0
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1992 chr1 81684 . T C 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.407;DP=37;Dels=0.00;FS=3.014;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=45.14;MQ0=1;MQRankSum=-3.850;QD=11.40;ReadPosRankSum=1.572;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:450,0,653
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1993 chr1 81688 . G A 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.027;DP=37;Dels=0.00;FS=3.014;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.14;MQ0=1;MQRankSum=-3.947;QD=10.94;ReadPosRankSum=2.054;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:433,0,686
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1994 chr1 81689 . T C 387.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.817;DP=36;Dels=0.00;FS=2.958;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.11;MQ0=1;MQRankSum=-3.750;QD=10.77;ReadPosRankSum=1.950;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:416,0,612
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1995 chr1 81693 . C T 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.747;DP=38;Dels=0.00;FS=4.815;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.42;MQ0=1;MQRankSum=-3.581;QD=12.68;ReadPosRankSum=1.143;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:510,0,642
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1996 chr1 81698 . T C 1307.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=44.87;MQ0=1;QD=30.86;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1336,105,0
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1997 chr1 81707 . T C 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.402;DP=47;Dels=0.00;FS=1.176;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.19;MQ0=1;MQRankSum=3.636;QD=11.87;ReadPosRankSum=-0.268;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:586,0,810
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1998 chr1 81724 . T C 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.003;DP=44;Dels=0.00;FS=1.986;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=46.23;MQ0=1;MQRankSum=-0.378;QD=1.27;ReadPosRankSum=0.609;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:36,8:44:84:84,0,1258
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1999 chr1 81739 . G A 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.481;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=46.48;MQ0=1;MQRankSum=-2.983;QD=19.66;ReadPosRankSum=0.454;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,28:42:99:854,0,419
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2000 chr1 81751 . G A 1532.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.00;MQ0=0;QD=26.66;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1561,114,0
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2001 chr1 81778 . A G 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.868;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.08;MQ0=3;MQRankSum=0.964;QD=8.94;ReadPosRankSum=2.043;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:493,0,1122
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2002 chr1 81794 . A C 1013.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.402;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.07;MQ0=3;MQRankSum=0.029;QD=18.77;ReadPosRankSum=-0.488;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,30:54:99:1042,0,496
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2003 chr1 81819 . A G 1360.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=45.13;MQ0=3;QD=31.65;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1389,105,0
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2004 chr1 81854 . T C 1085.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.60;MQ0=0;QD=30.67;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1114,84,0
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2005 chr1 81866 . G C 932.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.99;MQ0=0;QD=30.61;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,24:24:72:961,72,0
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2006 chr1 81879 . A G 1084.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=46.18;MQ0=0;QD=34.99;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,30:31:84:1113,84,0
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2007 chr1 81881 . G A 678.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=46.68;MQ0=0;MQRankSum=-0.097;QD=21.21;ReadPosRankSum=2.511;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:12,20:32:99:707,0,302
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2008 chr1 81889 . G A 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.311;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=49.01;MQ0=0;MQRankSum=-0.851;QD=9.17;ReadPosRankSum=-1.311;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,13:34:99:340,0,730
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2009 chr1 81914 . C T 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.672;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=51.95;MQ0=0;MQRankSum=0.503;QD=17.79;ReadPosRankSum=-3.004;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,22:40:99:740,0,520
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2010 chr1 81927 . C T 1565.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.72;MQ0=0;QD=28.57;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1594,123,0
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2011 chr1 81935 . A T 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.440;DP=43;Dels=0.00;FS=1.237;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.74;MQ0=0;MQRankSum=-0.335;QD=12.44;ReadPosRankSum=1.279;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,17:43:99:563,0,831
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2012 chr1 81947 . T A 1397.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.19;MQ0=0;QD=30.54;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1426,108,0
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2013 chr1 81948 . G C 1380.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.19;MQ0=0;QD=31.38;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1409,105,0
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2014 chr1 81951 . T C 1385.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.24;MQ0=0;QD=25.32;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,37:38:99:1414,105,0
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2015 chr1 81995 . G A 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.074;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=0;MQRankSum=-2.114;QD=12.73;ReadPosRankSum=0.458;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:512,0,740
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2016 chr1 82003 . A G 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.671;DP=37;Dels=0.00;FS=1.392;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-3.877;QD=9.37;ReadPosRankSum=3.261;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,12:37:99:375,0,858
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2017 chr1 82004 . A G 351.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.320;DP=37;Dels=0.00;FS=1.392;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-3.910;QD=9.51;ReadPosRankSum=3.326;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,12:37:99:380,0,857
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2018 chr1 82005 . G A 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.190;DP=37;Dels=0.00;FS=1.392;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-3.358;QD=9.53;ReadPosRankSum=3.293;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,12:37:99:381,0,863
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2019 chr1 82009 . T C 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.836;DP=36;Dels=0.00;FS=3.018;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=-3.574;QD=10.05;ReadPosRankSum=2.970;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,12:36:99:390,0,731
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2020 chr1 82011 . G C 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.763;DP=35;Dels=0.00;FS=1.421;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.35;MQ0=0;MQRankSum=-3.736;QD=10.42;ReadPosRankSum=2.763;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:393,0,756
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2021 chr1 82025 . T C 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.275;DP=40;Dels=0.00;FS=4.364;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.59;MQ0=0;MQRankSum=-4.604;QD=16.92;ReadPosRankSum=0.244;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,21:40:99:705,0,617
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2022 chr1 82036 . A G 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.824;DP=38;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.13;MQ0=0;MQRankSum=-4.538;QD=19.31;ReadPosRankSum=-0.103;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,22:38:99:762,0,463
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2023 chr1 82050 . C T 743.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.144;DP=35;Dels=0.00;FS=10.665;HaplotypeScore=49.2919;MLEAC=1;MLEAF=0.500;MQ=54.70;MQ0=0;MQRankSum=-4.080;QD=21.25;ReadPosRankSum=-1.280;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,22:35:99:772,0,401
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2024 chr1 82064 . T C 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.141;DP=31;Dels=0.00;FS=8.272;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-4.343;QD=19.41;ReadPosRankSum=1.501;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,18:31:99:630,0,427
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2025 chr1 82080 . C T 1151.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.78;MQ0=0;QD=29.06;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1180,87,0
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2026 chr1 82081 . C T 1143.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.78;MQ0=0;QD=27.94;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1172,87,0
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2027 chr1 82082 . A G 1146.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.78;MQ0=0;QD=28.52;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1175,87,0
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2028 chr1 82096 . T A 1128.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.09;MQ0=0;QD=29.16;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1157,93,0
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2029 chr1 82126 . G A 592.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.199;DP=37;Dels=0.00;FS=3.009;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=0;MQRankSum=-1.977;QD=16.02;ReadPosRankSum=-0.169;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:621,0,501
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2030 chr1 82156 . G A 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.862;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=0;MQRankSum=-0.011;QD=14.34;ReadPosRankSum=0.990;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:702,0,724
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2031 chr1 82158 . T A 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.151;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=0.352;QD=13.81;ReadPosRankSum=1.638;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:705,0,824
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2032 chr1 82161 . C G 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.171;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-0.131;QD=16.63;ReadPosRankSum=-1.578;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:843,0,731
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2033 chr1 82181 . T C 1791.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.84;MQ0=0;QD=33.17;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,50:51:99:1820,138,0
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2034 chr1 82212 . G A 941.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.113;DP=55;Dels=0.00;FS=1.075;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.87;MQ0=0;MQRankSum=-0.113;QD=17.12;ReadPosRankSum=0.788;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:970,0,654
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2035 chr1 82270 . A C 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.202;DP=48;Dels=0.00;FS=7.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=-0.969;QD=11.54;ReadPosRankSum=0.224;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,18:48:99:582,0,945
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2036 chr1 82315 . C T 1935.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=0;QD=33.36;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:1964,150,0
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2037 chr1 82352 . G C 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.790;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=0.780;QD=14.59;ReadPosRankSum=0.523;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:787,0,872
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2038 chr1 82367 . G A 907.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.433;DP=60;Dels=0.00;FS=0.988;HaplotypeScore=2.7001;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=0.509;QD=15.13;ReadPosRankSum=-0.630;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,28:60:99:936,0,959
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2039 chr1 82385 . G T 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.579;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=81.3181;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=-0.230;QD=0.21;ReadPosRankSum=-3.378;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:55,6:62:41:41,0,1896
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2040 chr1 82434 . T C 735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.253;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.61;MQ0=0;MQRankSum=-1.087;QD=14.15;ReadPosRankSum=1.842;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,23:52:99:764,0,957
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2041 chr1 82440 . G C 859.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.513;DP=49;Dels=0.00;FS=1.092;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.46;MQ0=0;MQRankSum=0.955;QD=17.55;ReadPosRankSum=-1.920;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:888,0,719
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2042 chr1 82482 . G A 740.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.010;DP=51;Dels=0.00;FS=1.064;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=57.36;MQ0=1;MQRankSum=-1.757;QD=14.52;ReadPosRankSum=-1.194;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,24:51:99:769,0,899
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2043 chr1 82487 . T A 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=50;Dels=0.00;FS=1.101;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=1;MQRankSum=-0.850;QD=15.32;ReadPosRankSum=-0.470;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:794,0,848
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2044 chr1 82613 . T C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.975;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=1;MQRankSum=-1.183;QD=12.44;ReadPosRankSum=0.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:675,0,964
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2045 chr1 82614 . A G 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.467;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=1;MQRankSum=-0.539;QD=12.44;ReadPosRankSum=0.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:675,0,934
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2046 chr1 82616 . G C 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.27;MQ0=1;MQRankSum=-2.266;QD=11.86;ReadPosRankSum=0.405;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,23:53:99:657,0,973
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2047 chr1 82648 . A G 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.315;DP=45;Dels=0.00;FS=5.254;HaplotypeScore=6.9393;MLEAC=1;MLEAF=0.500;MQ=52.78;MQ0=3;MQRankSum=-4.177;QD=3.93;ReadPosRankSum=-0.286;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,12:45:99:205,0,1095
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2048 chr1 82650 . T C 107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.065;DP=43;Dels=0.00;FS=5.772;HaplotypeScore=4.9694;MLEAC=1;MLEAF=0.500;MQ=52.57;MQ0=3;MQRankSum=-4.146;QD=2.51;ReadPosRankSum=0.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,10:43:99:136,0,1090
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2049 chr1 82656 . G A 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.901;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=4.9694;MLEAC=1;MLEAF=0.500;MQ=52.02;MQ0=3;MQRankSum=4.699;QD=22.29;ReadPosRankSum=0.901;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,27:41:99:942,0,189
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2050 chr1 82658 . T G 111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.383;DP=42;Dels=0.00;FS=3.333;HaplotypeScore=4.9694;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=3;MQRankSum=-4.050;QD=2.66;ReadPosRankSum=-1.617;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,12:42:99:140,0,1017
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2051 chr1 82668 . A C 1112.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=52.88;MQ0=3;QD=30.91;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,36:36:90:1141,90,0
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2052 chr1 82690 . G T 345.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.521;DP=40;Dels=0.00;FS=5.301;HaplotypeScore=0.9867;MLEAC=1;MLEAF=0.500;MQ=56.01;MQ0=1;MQRankSum=-2.041;QD=8.64;ReadPosRankSum=-2.488;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,14:40:99:374,0,898
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2053 chr1 82792 . T A 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.636;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=0.289;QD=19.32;ReadPosRankSum=-0.834;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:743,0,494
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2054 chr1 82795 . T C 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.055;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=-0.114;QD=11.86;ReadPosRankSum=1.314;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,15:37:99:467,0,769
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2055 chr1 82814 . G A 330.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.079;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=1;MQRankSum=0.958;QD=8.48;ReadPosRankSum=0.707;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:359,0,871
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2056 chr1 82877 . T C 1238.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.481;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=2.5775;MLEAC=2;MLEAF=1.00;MQ=59.05;MQ0=0;MQRankSum=0.385;QD=34.41;ReadPosRankSum=1.444;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:1,35:36:67:1267,67,0
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2057 chr1 82878 . C T 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.053;DP=36;Dels=0.00;FS=2.928;HaplotypeScore=2.5775;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-0.111;QD=15.72;ReadPosRankSum=-2.244;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,20:36:99:594,0,499
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2058 chr1 82887 . T C 410.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.631;DP=36;Dels=0.00;FS=1.344;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-0.257;QD=11.41;ReadPosRankSum=2.246;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:439,0,686
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2059 chr1 82936 . A T 196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.839;DP=28;Dels=0.00;FS=10.544;HaplotypeScore=8.7318;MLEAC=1;MLEAF=0.500;MQ=58.58;MQ0=0;MQRankSum=-0.839;QD=7.03;ReadPosRankSum=1.551;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,8:28:99:225,0,697
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|
|
2060 chr1 82937 . G A 1059.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=7.7653;MLEAC=2;MLEAF=1.00;MQ=58.58;MQ0=0;QD=29.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1088,84,0
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|
|
2061 chr1 82946 . A G 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.977;DP=34;Dels=0.00;FS=20.808;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=1.942;QD=14.52;ReadPosRankSum=1.353;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,19:34:99:522,0,487
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|
|
2062 chr1 82981 . A C 1508.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=33.7746;MLEAC=2;MLEAF=1.00;MQ=57.89;MQ0=0;QD=32.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1537,117,0
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|
|
2063 chr1 83013 . A T 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.717;DP=48;Dels=0.00;FS=46.456;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=-1.792;QD=11.70;ReadPosRankSum=0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,19:48:99:590,0,915
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|
|
2064 chr1 83024 . A G 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.067;DP=42;Dels=0.00;FS=42.658;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=1;MQRankSum=-2.045;QD=10.57;ReadPosRankSum=0.468;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:472,0,804
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|
|
2065 chr1 83033 . A G 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.157;DP=39;Dels=0.00;FS=31.330;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.45;MQ0=1;MQRankSum=-3.862;QD=6.79;ReadPosRankSum=2.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,12:39:99:293,0,843
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|
|
2066 chr1 83044 . C T 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.349;DP=37;Dels=0.00;FS=27.416;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=54.13;MQ0=1;MQRankSum=-4.362;QD=6.40;ReadPosRankSum=2.278;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,11:37:99:265,0,839
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|
|
2067 chr1 83083 . T C 872.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.31;MQ0=0;QD=27.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,23:23:66:901,66,0
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|
|
2068 chr1 83091 . A G 855.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;QD=28.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:884,66,0
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|
|
2069 chr1 83162 . C T 653.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9867;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,18:18:51:682,51,0
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|
|
2070 chr1 83337 . A C 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.588;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.48;MQ0=1;MQRankSum=-2.646;QD=10.34;ReadPosRankSum=-1.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_5_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83279_83401) GT:AD:DP:GQ:PL 0/1:9,8:17:99:204,0,330
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|
2071 chr1 83398 . G T 94.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.192;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=3.9845;MLEAC=1;MLEAF=0.500;MQ=47.10;MQ0=1;MQRankSum=0.778;QD=6.32;ReadPosRankSum=2.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_5_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83279_83401) GT:AD:DP:GQ:PL 0/1:11,4:15:99:123,0,311
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|
2072 chr1 83404 . G A 60.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.083;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=3.9845;MLEAC=1;MLEAF=0.500;MQ=45.65;MQ0=1;MQRankSum=-1.157;QD=4.34;ReadPosRankSum=-1.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:9,5:14:89:89,0,317
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|
|
2073 chr1 83532 . G T 196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.264;DP=30;Dels=0.00;FS=5.946;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.56;MQ0=2;MQRankSum=-3.188;QD=6.56;ReadPosRankSum=1.894;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_5_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83509_83569) GT:AD:DP:GQ:PL 0/1:18,12:30:99:225,0,597
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2074 chr1 83605 . A G 62.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.633;DP=24;Dels=0.00;FS=7.799;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.85;MQ0=0;MQRankSum=-2.167;QD=2.62;ReadPosRankSum=1.233;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,6:24:91:91,0,606
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|
2075 chr1 83629 . T G 38.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.602;DP=19;Dels=0.00;FS=4.713;HaplotypeScore=1.7880;MLEAC=1;MLEAF=0.500;MQ=41.28;MQ0=0;MQRankSum=-2.268;QD=2.04;ReadPosRankSum=-1.991;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,5:19:67:67,0,465
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|
2076 chr1 83691 . T G 192.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.137;DP=35;Dels=0.00;FS=8.175;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=42.05;MQ0=0;MQRankSum=-0.020;QD=5.51;ReadPosRankSum=-1.552;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,8:35:99:221,0,947
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|
2077 chr1 83704 . C T 1319.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.35;MQ0=1;QD=32.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1348,102,0
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|
2078 chr1 83837 . G A 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.636;DP=30;Dels=0.00;FS=14.239;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.28;MQ0=2;MQRankSum=-3.738;QD=5.23;ReadPosRankSum=-0.788;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L4|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83730_84064) GT:AD:DP:GQ:PL 0/1:20,10:30:99:185,0,667
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2079 chr1 84090 . G T 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.235;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=2.8663;MLEAC=1;MLEAF=0.500;MQ=55.21;MQ0=0;MQRankSum=0.440;QD=13.44;ReadPosRankSum=-0.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:539,0,732
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|
2080 chr1 84156 . C T 1240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.552;DP=56;Dels=0.00;FS=6.157;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.20;MQ0=0;MQRankSum=-1.818;QD=22.16;ReadPosRankSum=0.463;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,39:56:99:1269,0,542
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2081 chr1 84243 . G A 1544.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=36.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1573,120,0
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|
2082 chr1 84266 . A C 455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.232;DP=41;Dels=0.00;FS=2.837;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.392;QD=11.12;ReadPosRankSum=-0.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:484,0,881
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2083 chr1 84467 . C A 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.341;DP=48;Dels=0.00;FS=5.874;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-0.321;QD=14.87;ReadPosRankSum=1.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,22:48:99:742,0,877
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2084 chr1 84548 . G T 1008.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.339;DP=61;Dels=0.00;FS=3.670;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=2.402;QD=16.54;ReadPosRankSum=1.854;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,30:61:99:1037,0,988
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2085 chr1 84596 . C T 2308.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.50;MQ0=0;QD=26.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2337,178,0
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2086 chr1 84601 . C T 1275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.270;DP=65;Dels=0.00;FS=2.135;HaplotypeScore=1.9664;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=1.172;QD=19.63;ReadPosRankSum=-0.797;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,39:65:99:1304,0,773
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2087 chr1 84805 . A G 972.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.168;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=0;MQRankSum=0.505;QD=19.46;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S113|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 0/1:20,30:50:99:1001,0,641
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2088 chr1 84858 . A C 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.541;DP=42;Dels=0.00;FS=8.832;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-1.322;QD=16.95;ReadPosRankSum=1.876;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aCa|K131T|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 0/1:20,22:42:99:740,0,673
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2089 chr1 84868 . C T 1590.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=0;QD=28.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V134|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1619,123,0
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2090 chr1 84880 . G A 1477.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.91;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L138|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1506,114,0
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2091 chr1 84886 . A G 568.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.437;DP=39;Dels=0.00;FS=1.261;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.521;QD=14.58;ReadPosRankSum=-0.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V140|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 0/1:21,18:39:99:597,0,712
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2092 chr1 85016 . G A 959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.600;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.347;QD=17.45;ReadPosRankSum=-0.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:988,0,847
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2093 chr1 85055 . A G 963.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.265;DP=59;Dels=0.00;FS=7.450;HaplotypeScore=2.4875;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=0.599;QD=16.34;ReadPosRankSum=0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:992,0,999
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2094 chr1 85064 . T C 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.086;DP=54;Dels=0.00;FS=3.998;HaplotypeScore=2.4875;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=1.488;QD=14.61;ReadPosRankSum=0.311;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,27:54:99:817,0,887
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2095 chr1 85114 . A G 770.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.117;DP=47;Dels=0.00;FS=2.488;HaplotypeScore=1.9662;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=-1.011;QD=16.40;ReadPosRankSum=-0.947;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:799,0,742
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2096 chr1 85206 . A G 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.867;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.7465;MLEAC=1;MLEAF=0.500;MQ=60.20;MQ0=0;MQRankSum=-0.412;QD=14.65;ReadPosRankSum=-1.338;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:834,0,932
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2097 chr1 85257 . C T 2136.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=60.19;MQ0=0;QD=25.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,55:56:99:2165,163,0
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2098 chr1 85259 . T C 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.311;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=26.7919;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.070;QD=17.50;ReadPosRankSum=0.552;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1043,0,924
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2099 chr1 85307 . G T 2188.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.18;MQ0=0;QD=23.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2217,166,0
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2100 chr1 85388 . T C 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.676;DP=56;Dels=0.00;FS=2.338;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.972;QD=17.91;ReadPosRankSum=2.060;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,31:56:99:1031,0,826
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2101 chr1 85403 . A G 1059.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.803;DP=53;Dels=0.00;FS=3.822;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.045;QD=20.00;ReadPosRankSum=1.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,31:53:99:1088,0,713
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2102 chr1 85446 . T G 2073.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2102,157,0
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2103 chr1 85454 . C A 1996.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:2025,150,0
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2104 chr1 85460 . A C 857.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.217;DP=48;Dels=0.00;FS=4.180;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.445;QD=17.87;ReadPosRankSum=-2.121;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:886,0,741
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2105 chr1 85552 . A C 1841.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.662;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=0.742;QD=31.35;ReadPosRankSum=-0.035;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:1,48:49:99:1870,141,0
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2106 chr1 85658 . T A 531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.903;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=2.2566;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=-0.933;QD=12.97;ReadPosRankSum=2.850;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:560,0,680
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2107 chr1 85709 . T A 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.209;DP=30;Dels=0.00;FS=3.431;HaplotypeScore=15.9845;MLEAC=1;MLEAF=0.500;MQ=58.03;MQ0=0;MQRankSum=-0.209;QD=17.76;ReadPosRankSum=1.590;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:561,0,349
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2108 chr1 85779 . A G 200.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.928;DP=32;Dels=0.00;FS=10.207;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=0.042;QD=6.27;ReadPosRankSum=0.922;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,9:32:99:229,0,795
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2109 chr1 85837 . A T 1322.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1351,102,0
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2110 chr1 85866 . G A 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.539;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=15.4975;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.788;QD=15.93;ReadPosRankSum=-1.286;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,15:30:99:506,0,472
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2111 chr1 85928 . G A 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.190;DP=31;Dels=0.00;FS=1.566;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.021;QD=22.54;ReadPosRankSum=1.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:10,21:31:99:727,0,300
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2112 chr1 85964 . T C 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.066;DP=32;Dels=0.00;FS=3.848;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.936;QD=26.59;ReadPosRankSum=-0.065;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:8,24:32:99:879,0,222
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2113 chr1 85983 . T C 764.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.371;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.457;QD=24.67;ReadPosRankSum=-0.196;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,22:31:99:793,0,280
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2114 chr1 85984 . A T 749.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.024;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.6671;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.413;QD=24.19;ReadPosRankSum=-0.326;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,22:31:99:778,0,283
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2115 chr1 86057 . T A 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.649;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=1.117;QD=16.34;ReadPosRankSum=-0.819;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:796,0,802
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2116 chr1 86096 . T C 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.383;DP=47;Dels=0.00;FS=6.396;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.57;MQ0=0;MQRankSum=1.171;QD=18.42;ReadPosRankSum=0.952;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:894,0,583
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2117 chr1 86197 . A G 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.957;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.775;QD=15.83;ReadPosRankSum=1.413;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:614,0,592
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2118 chr1 86283 . T G 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.233;DP=81;Dels=0.00;FS=11.183;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.22;MQ0=1;MQRankSum=-1.581;QD=7.98;ReadPosRankSum=-5.926;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:45,36:81:99:675,0,1045
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2119 chr1 86295 . G A 212.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.399;DP=79;Dels=0.00;FS=0.000;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=1;MQRankSum=-0.694;QD=2.69;ReadPosRankSum=-1.111;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:61,17:79:99:241,0,1690
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2120 chr1 86334 . C T 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.178;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=1;MQRankSum=-1.600;QD=18.65;ReadPosRankSum=0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,29:49:99:942,0,629
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2121 chr1 86368 . T C 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.611;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.010;QD=17.87;ReadPosRankSum=-0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:904,0,769
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2122 chr1 86487 . C T 1135.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.006;DP=60;Dels=0.00;FS=3.617;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-2.588;QD=18.93;ReadPosRankSum=1.410;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,34:60:99:1164,0,811
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2123 chr1 86494 . G A 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.597;DP=62;Dels=0.00;FS=1.012;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-1.077;QD=11.83;ReadPosRankSum=-0.282;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,24:62:99:762,0,1311
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2124 chr1 86710 . C T 638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.161;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.952;QD=15.58;ReadPosRankSum=-1.135;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:667,0,725
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2125 chr1 86780 . T C 1962.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1991,150,0
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2126 chr1 86783 . T C 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.254;DP=51;Dels=0.00;FS=1.083;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.612;QD=15.98;ReadPosRankSum=0.141;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:843,0,891
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2127 chr1 86812 . C G 2201.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.85;MQ0=0;QD=28.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2230,172,0
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2128 chr1 86874 . T C 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.055;DP=46;Dels=0.00;FS=2.444;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=0.587;QD=18.63;ReadPosRankSum=0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,26:46:99:885,0,605
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2129 chr1 86928 . A T 1814.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.80;MQ0=0;QD=28.24;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1843,138,0
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2130 chr1 86945 . C T 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.551;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.651;QD=15.59;ReadPosRankSum=-1.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:792,0,917
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2131 chr1 87016 . C T 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.274;DP=53;Dels=0.00;FS=2.380;HaplotypeScore=46.7458;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.134;QD=15.01;ReadPosRankSum=0.597;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:824,0,910
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2132 chr1 87161 . A G 1557.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=15.2776;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.61;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1586,117,0
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2133 chr1 87182 . A G 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.190;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=65.7226;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.562;QD=16.77;ReadPosRankSum=-1.948;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:716,0,647
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2134 chr1 87257 . T C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.809;DP=42;Dels=0.00;FS=2.756;HaplotypeScore=3.9986;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.202;QD=14.71;ReadPosRankSum=-0.455;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,19:42:99:646,0,809
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2135 chr1 87282 . C T 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.910;DP=42;Dels=0.00;FS=11.850;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.581;QD=17.97;ReadPosRankSum=-0.708;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:783,0,641
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2136 chr1 87399 . T A 662.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.840;DP=43;Dels=0.00;FS=4.388;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.426;QD=15.41;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:691,0,818
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2137 chr1 87964 . T C 1652.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=59.27;MQ0=0;QD=31.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R2079|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_87910_88146) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1681,126,0
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2138 chr1 88214 . A G 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.856;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=3.4710;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=1.316;QD=17.04;ReadPosRankSum=2.984;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,23:45:99:795,0,623
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2139 chr1 88242 . A C 1458.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9734;MLEAC=2;MLEAF=1.00;MQ=59.07;MQ0=0;QD=31.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1487,111,0
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2140 chr1 88243 . G A 786.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.274;DP=40;Dels=0.00;FS=2.817;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=0.465;QD=19.67;ReadPosRankSum=-2.818;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:17,23:40:99:815,0,487
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2141 chr1 88460 . C T 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.222;DP=41;Dels=0.00;FS=4.561;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.874;QD=15.80;ReadPosRankSum=-0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:676,0,700
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2142 chr1 88534 . T C 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.499;DP=50;Dels=0.00;FS=13.391;HaplotypeScore=1.6643;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=0.545;QD=14.54;ReadPosRankSum=-1.363;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q1964|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_88510_88890) GT:AD:DP:GQ:PL 0/1:27,23:50:99:755,0,913
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2143 chr1 88912 . A C 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.131;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=-1.268;QD=13.31;ReadPosRankSum=-0.971;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:627,0,862
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2144 chr1 88959 . C T 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.476;DP=56;Dels=0.00;FS=9.559;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.79;MQ0=0;MQRankSum=-0.590;QD=15.78;ReadPosRankSum=0.574;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,27:56:99:912,0,1002
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2145 chr1 88961 . C G 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.381;DP=58;Dels=0.00;FS=11.723;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=0.661;QD=17.50;ReadPosRankSum=-0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1043,0,950
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2146 chr1 88987 . A G 2405.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=59.64;MQ0=0;QD=30.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2434,184,0
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2147 chr1 89344 . G C 1022.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.526;DP=61;Dels=0.00;FS=5.322;HaplotypeScore=2.9937;MLEAC=1;MLEAF=0.500;MQ=56.95;MQ0=1;MQRankSum=-0.052;QD=16.77;ReadPosRankSum=-0.304;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1051,0,895
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2148 chr1 89418 . A T 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.659;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=0;MQRankSum=0.521;QD=18.45;ReadPosRankSum=0.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggA|G1793|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89391_89495) GT:AD:DP:GQ:PL 0/1:19,25:44:99:840,0,514
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2149 chr1 89522 . A G 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.620;DP=45;Dels=0.00;FS=11.478;HaplotypeScore=103.5819;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-0.517;QD=13.15;ReadPosRankSum=-1.321;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,19:45:99:620,0,881
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2150 chr1 89531 . A G 56.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.825;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=114.0798;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=1;MQRankSum=-0.041;QD=1.14;ReadPosRankSum=-1.853;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:41,9:50:85:85,0,1381
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2151 chr1 89635 . T G 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.207;DP=56;Dels=0.00;FS=7.797;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.737;QD=18.12;ReadPosRankSum=0.339;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Cat|N1762H|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89618_89905) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1043,0,749
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2152 chr1 89720 . T C 1891.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.88;MQ0=0;QD=30.77;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q1733|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89618_89905) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1920,144,0
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2153 chr1 89745 . A G 1759.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M1725T|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89618_89905) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1788,135,0
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2154 chr1 89792 . G A 2016.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V1709|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89618_89905) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2045,159,0
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2155 chr1 89954 . T C 1227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.449;DP=64;Dels=0.00;FS=2.069;HaplotypeScore=2.6551;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.884;QD=19.18;ReadPosRankSum=1.359;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,37:64:99:1256,0,894
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2156 chr1 90005 . A G 1150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.267;DP=58;Dels=0.00;FS=3.623;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.523;QD=19.84;ReadPosRankSum=0.502;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1179,0,842
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2157 chr1 90289 . C T 1801.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1597T|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_90065_90416) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1830,141,0
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2158 chr1 90303 . A G 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.343;DP=46;Dels=0.00;FS=5.030;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.388;QD=13.49;ReadPosRankSum=0.720;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I1592T|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_90065_90416) GT:AD:DP:GQ:PL 0/1:26,20:46:99:649,0,883
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2159 chr1 90520 . C T 496.84 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.063;DP=21;Dels=0.00;FS=7.375;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=56.05;MQ0=1;MQRankSum=-0.693;QD=23.66;ReadPosRankSum=2.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:3,18:21:18:525,0,18
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2160 chr1 90521 . C T 488.03 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.441;DP=21;Dels=0.00;FS=8.316;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=56.05;MQ0=1;MQRankSum=-1.197;QD=23.24;ReadPosRankSum=2.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:3,18:21:12:516,0,12
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2161 chr1 90525 . C T 577.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=43.4929;MLEAC=2;MLEAF=1.00;MQ=55.62;MQ0=1;QD=30.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:1,18:19:51:606,51,0
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2162 chr1 90567 . G A 583.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=15.0334;MLEAC=2;MLEAF=1.00;MQ=56.91;MQ0=0;QD=34.34;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,17:17:48:612,48,0
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2163 chr1 90588 . A G 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.589;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=3.1875;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=1.768;QD=8.06;ReadPosRankSum=-0.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,9:29:99:262,0,686
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2164 chr1 90590 . T C 1086.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=3.1875;MLEAC=2;MLEAF=1.00;MQ=57.35;MQ0=0;QD=24.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1115,84,0
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2165 chr1 90591 . G A 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.430;DP=30;Dels=0.00;FS=1.987;HaplotypeScore=3.1875;MLEAC=1;MLEAF=0.500;MQ=57.44;MQ0=0;MQRankSum=0.387;QD=21.59;ReadPosRankSum=0.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,19:30:99:676,0,304
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2166 chr1 90977 . G T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.999;DP=45;Dels=0.00;FS=4.453;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=-0.857;QD=13.48;ReadPosRankSum=-1.633;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:635,0,845
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2167 chr1 90985 . T C 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.358;DP=47;Dels=0.00;FS=4.385;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=1.160;QD=12.29;ReadPosRankSum=0.228;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:606,0,909
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2168 chr1 91106 . T C 1596.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.51;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1625,120,0
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2169 chr1 91526 . G C 509.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.453;DP=42;Dels=0.00;FS=2.865;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.065;QD=12.14;ReadPosRankSum=-0.842;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:538,0,882
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2170 chr1 91614 . A C 984.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.414;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.445;QD=17.90;ReadPosRankSum=0.735;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:1013,0,821
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2171 chr1 91617 . T A 1018.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.797;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.288;QD=18.19;ReadPosRankSum=1.043;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,30:56:99:1047,0,834
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2172 chr1 91650 . C A 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.554;DP=42;Dels=0.00;FS=1.831;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.893;QD=0.88;ReadPosRankSum=-2.796;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q1346H|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91645_91760) GT:AD:DP:GQ:PL 0/1:37,5:42:65:65,0,1325
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2173 chr1 91722 . A T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.741;DP=50;Dels=0.00;FS=4.367;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.000;QD=10.08;ReadPosRankSum=0.676;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggA|G1322|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91645_91760) GT:AD:DP:GQ:PL 0/1:33,17:50:99:532,0,996
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2174 chr1 91774 . G A 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.165;DP=60;Dels=0.00;FS=1.043;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.765;QD=13.25;ReadPosRankSum=-1.230;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,25:60:99:823,0,1195
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2175 chr1 91973 . C T 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.524;DP=42;Dels=0.00;FS=8.623;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.239;QD=15.71;ReadPosRankSum=-1.901;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1269|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:20,22:42:99:688,0,658
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2176 chr1 91976 . G A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.609;DP=46;Dels=0.00;FS=6.133;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.277;QD=12.97;ReadPosRankSum=2.338;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1268|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:26,20:46:99:625,0,846
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2177 chr1 92011 . A C 1093.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.455;DP=56;Dels=0.00;FS=7.262;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.813;QD=19.53;ReadPosRankSum=1.995;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S1257A|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1122,0,788
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2178 chr1 92186 . G A 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.573;DP=35;Dels=0.00;FS=5.368;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.083;QD=16.51;ReadPosRankSum=-0.083;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S1198|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:16,19:35:99:606,0,541
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2179 chr1 92279 . A G 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.565;DP=41;Dels=0.00;FS=6.803;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.090;QD=18.92;ReadPosRankSum=0.775;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,23:41:99:804,0,592
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2180 chr1 92300 . C G 1407.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.55;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1436,108,0
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2181 chr1 92325 . T C 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.810;DP=44;Dels=0.00;FS=6.673;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.692;QD=16.40;ReadPosRankSum=-0.951;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:750,0,740
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2182 chr1 92362 . A G 723.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.701;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.214;QD=14.48;ReadPosRankSum=0.097;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:752,0,920
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2183 chr1 92420 . A C 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.072;DP=46;Dels=0.00;FS=6.635;HaplotypeScore=12.9977;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.404;QD=10.39;ReadPosRankSum=0.519;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,16:46:99:506,0,1054
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2184 chr1 92426 . C T 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.734;DP=42;Dels=0.00;FS=9.664;HaplotypeScore=12.9977;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-0.680;QD=9.99;ReadPosRankSum=0.494;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,14:42:99:448,0,1021
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2185 chr1 92459 . G A 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=41;Dels=0.00;FS=2.858;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.521;QD=11.87;ReadPosRankSum=-0.174;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:515,0,892
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2186 chr1 92463 . G A 558.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.308;DP=43;Dels=0.00;FS=2.743;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-0.406;QD=12.99;ReadPosRankSum=-0.529;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:587,0,880
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2187 chr1 92529 . T A 955.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=1.253;QD=16.77;ReadPosRankSum=0.503;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:984,0,918
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2188 chr1 92647 . A G 394.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-0.840;QD=9.40;ReadPosRankSum=0.680;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,14:42:99:423,0,976
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2189 chr1 92758 . T A 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.338;DP=53;Dels=0.00;FS=3.955;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=0.930;QD=10.18;ReadPosRankSum=1.380;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:568,0,1136
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2190 chr1 92787 . A G 917.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=68;Dels=0.00;FS=3.335;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=0;MQRankSum=0.142;QD=13.50;ReadPosRankSum=0.377;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,30:68:99:946,0,1223
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2191 chr1 92856 . G C 2242.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=57.58;MQ0=1;QD=29.11;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2271,172,0
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2192 chr1 92881 . G T 1034.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.472;DP=57;Dels=0.00;FS=9.783;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=1;MQRankSum=1.051;QD=18.15;ReadPosRankSum=-0.803;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1063,0,740
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2193 chr1 92887 . A G 874.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.408;DP=56;Dels=0.00;FS=2.506;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.89;MQ0=1;MQRankSum=0.126;QD=15.62;ReadPosRankSum=0.008;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,30:56:99:903,0,715
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2194 chr1 92906 . T C 862.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.983;DP=64;Dels=0.00;FS=2.137;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.08;MQ0=2;MQRankSum=1.450;QD=13.48;ReadPosRankSum=0.728;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,30:64:99:891,0,1127
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2195 chr1 93051 . G C 1300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.778;DP=67;Dels=0.00;FS=0.945;HaplotypeScore=2.9966;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=1.436;QD=19.41;ReadPosRankSum=-0.576;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,38:67:99:1329,0,959
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2196 chr1 93126 . T G 1178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.582;DP=54;Dels=0.00;FS=5.804;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-0.349;QD=21.83;ReadPosRankSum=-0.099;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,34:54:99:1207,0,605
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2197 chr1 93129 . C T 1188.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.066;DP=54;Dels=0.00;FS=5.804;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=0.905;QD=22.01;ReadPosRankSum=0.242;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,34:54:99:1217,0,604
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2198 chr1 93143 . G C 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.109;DP=51;Dels=0.00;FS=2.448;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.287;QD=11.86;ReadPosRankSum=-1.357;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,20:51:99:633,0,1071
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2199 chr1 93221 . G C 960.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=59;Dels=0.00;FS=0.998;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.371;QD=16.28;ReadPosRankSum=0.387;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:989,0,965
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2200 chr1 93235 . G A 1138.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.352;DP=63;Dels=0.00;FS=2.089;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=1.110;QD=18.08;ReadPosRankSum=-0.779;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,34:63:99:1167,0,900
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2201 chr1 93270 . T C 2111.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.10;MQ0=0;QD=30.32;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2140,160,0
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2202 chr1 93280 . T C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.487;DP=52;Dels=0.00;FS=4.010;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=1.194;QD=13.11;ReadPosRankSum=3.543;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:710,0,1066
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2203 chr1 93282 . G C 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.616;DP=49;Dels=0.00;FS=4.055;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=0.636;QD=14.02;ReadPosRankSum=3.222;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:715,0,961
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2204 chr1 93283 . G A 717.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.394;DP=50;Dels=0.00;FS=2.447;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.10;MQ0=0;MQRankSum=-1.065;QD=14.36;ReadPosRankSum=2.746;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:746,0,976
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2205 chr1 93306 . A T 2098.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.20;MQ0=0;QD=32.01;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2127,160,0
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2206 chr1 93333 . C T 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.258;DP=53;Dels=0.00;FS=5.940;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.20;MQ0=0;MQRankSum=0.454;QD=15.32;ReadPosRankSum=0.330;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:840,0,924
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2207 chr1 93352 . T C 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.393;DP=57;Dels=0.00;FS=11.817;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=60.19;MQ0=0;MQRankSum=-0.745;QD=15.03;ReadPosRankSum=1.402;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:885,0,1090
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2208 chr1 93358 . A C 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.132;DP=56;Dels=0.00;FS=12.410;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.19;MQ0=0;MQRankSum=-0.231;QD=14.50;ReadPosRankSum=1.615;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:840,0,1093
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2209 chr1 93504 . G A 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.233;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.560;QD=16.00;ReadPosRankSum=-0.653;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,29:59:99:972,0,962
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2210 chr1 93508 . G C 2130.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=2.9988;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.10;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2159,163,0
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2211 chr1 93567 . A G 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=59;Dels=0.00;FS=2.347;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.177;QD=9.56;ReadPosRankSum=0.344;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:39,20:59:99:592,0,1326
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2212 chr1 93595 . G A 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.874;DP=49;Dels=0.00;FS=4.620;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.830;QD=7.95;ReadPosRankSum=-0.586;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,14:49:99:418,0,1282
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2213 chr1 93676 . A G 942.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.901;DP=55;Dels=0.00;FS=1.026;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.019;QD=17.14;ReadPosRankSum=1.372;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F1167|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93628_93699) GT:AD:DP:GQ:PL 0/1:27,28:55:99:971,0,908
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2214 chr1 93754 . T A 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.413;DP=58;Dels=0.00;FS=5.597;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.191;QD=11.58;ReadPosRankSum=-0.111;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,23:58:99:700,0,1216
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2215 chr1 93879 . T C 1833.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.96;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1137|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93813_93975) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1862,141,0
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2216 chr1 93903 . G T 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.782;DP=45;Dels=0.00;FS=8.659;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.011;QD=16.62;ReadPosRankSum=-0.261;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atA|I1129|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93813_93975) GT:AD:DP:GQ:PL 0/1:22,23:45:99:776,0,668
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2217 chr1 93906 . C T 679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.482;DP=47;Dels=0.00;FS=6.054;HaplotypeScore=1.9830;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.098;QD=14.46;ReadPosRankSum=0.309;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K1128|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93813_93975) GT:AD:DP:GQ:PL 0/1:25,22:47:99:708,0,860
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2218 chr1 93998 . A G 2112.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=2.5774;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.68;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2141,163,0
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2219 chr1 94001 . A G 893.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.276;DP=53;Dels=0.00;FS=2.323;HaplotypeScore=1.5782;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.240;QD=16.86;ReadPosRankSum=0.827;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,27:53:99:922,0,890
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2220 chr1 94020 . G C 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.912;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.331;QD=15.44;ReadPosRankSum=1.733;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:785,0,888
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2221 chr1 94164 . A G 839.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.633;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.879;QD=15.00;ReadPosRankSum=-0.501;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y1084|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94102_94193) GT:AD:DP:GQ:PL 0/1:30,26:56:99:868,0,1033
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2222 chr1 94307 . G A 847.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.017;DP=48;Dels=0.00;FS=1.133;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.403;QD=17.66;ReadPosRankSum=-0.631;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:876,0,754
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2223 chr1 94331 . G T 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.887;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.692;QD=15.95;ReadPosRankSum=-0.109;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:714,0,748
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2224 chr1 94476 . G T 1018.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.404;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=1;MQRankSum=0.350;QD=18.87;ReadPosRankSum=-1.498;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,31:54:99:1047,0,739
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2225 chr1 94499 . C T 760.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.740;DP=55;Dels=0.00;FS=1.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=1;MQRankSum=0.531;QD=13.83;ReadPosRankSum=0.218;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,24:55:99:789,0,1061
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2226 chr1 94679 . A G 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.046;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=1.7334;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.612;QD=15.70;ReadPosRankSum=-0.198;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L1005|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94543_94708) GT:AD:DP:GQ:PL 0/1:26,25:51:99:829,0,859
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2227 chr1 94743 . G A 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.225;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=2.3122;MLEAC=1;MLEAF=0.500;MQ=61.17;MQ0=0;MQRankSum=-1.258;QD=9.38;ReadPosRankSum=3.272;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,12:36:99:366,0,807
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2228 chr1 94753 . A C 357.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.995;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=3.8896;MLEAC=1;MLEAF=0.500;MQ=61.17;MQ0=0;MQRankSum=-0.225;QD=9.94;ReadPosRankSum=0.898;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:386,0,718
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2229 chr1 94840 . A C 753.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.135;DP=58;Dels=0.00;FS=0.999;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-1.272;QD=13.00;ReadPosRankSum=-0.455;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S985A|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94808_94919) GT:AD:DP:GQ:PL 0/1:33,25:58:99:782,0,1167
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2230 chr1 94856 . C T 1026.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.053;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.040;QD=18.01;ReadPosRankSum=0.523;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L979|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94808_94919) GT:AD:DP:GQ:PL 0/1:25,32:57:99:1055,0,767
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2231 chr1 94898 . G A 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.088;DP=57;Dels=0.00;FS=2.219;HaplotypeScore=1.6649;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.679;QD=16.35;ReadPosRankSum=-2.038;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L965|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94808_94919) GT:AD:DP:GQ:PL 0/1:27,30:57:99:960,0,917
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2232 chr1 94963 . C A 867.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.638;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.668;QD=16.69;ReadPosRankSum=-0.503;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:896,0,874
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2233 chr1 94973 . A T 2138.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.12;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2167,163,0
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2234 chr1 95134 . T C 2154.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.28;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T933A|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_95058_95208) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2183,169,0
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2235 chr1 95594 . A G 912.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.180;DP=53;Dels=0.00;FS=5.738;HaplotypeScore=2.6552;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=1;MQRankSum=0.085;QD=17.22;ReadPosRankSum=0.349;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G817|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_95323_95596) GT:AD:DP:GQ:PL 0/1:24,28:53:99:941,0,742
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2236 chr1 95809 . G A 1511.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.57;MQ0=0;QD=34.54;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1540,114,0
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2237 chr1 96016 . C T 1313.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.43;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1342,99,0
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2238 chr1 96111 . A C 1249.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.76;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1278,96,0
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2239 chr1 96124 . A G 1357.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.72;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1386,105,0
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2240 chr1 96214 . A T 1007.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.364;DP=67;Dels=0.00;FS=6.694;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=0.622;QD=15.04;ReadPosRankSum=0.321;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,31:67:99:1036,0,1067
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2241 chr1 96224 . G A 924.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.166;DP=61;Dels=0.00;FS=3.561;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=0;MQRankSum=0.656;QD=15.16;ReadPosRankSum=-2.171;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,30:61:99:953,0,1050
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2242 chr1 96308 . T C 2053.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=28.62;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2082,154,0
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2243 chr1 96309 . A G 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.522;DP=54;Dels=0.00;FS=7.971;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.262;QD=13.66;ReadPosRankSum=-2.029;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:766,0,1037
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2244 chr1 96335 . G T 1948.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=0;QD=30.44;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:1977,147,0
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2245 chr1 96360 . G A 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.447;DP=58;Dels=0.00;FS=3.832;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=1.081;QD=15.86;ReadPosRankSum=-0.864;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:948,0,883
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2246 chr1 96399 . T G 905.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.085;DP=51;Dels=0.00;FS=8.273;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=1.902;QD=17.76;ReadPosRankSum=1.618;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:934,0,788
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2247 chr1 96448 . G A 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.536;DP=51;Dels=0.00;FS=4.093;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=1.121;QD=17.09;ReadPosRankSum=-1.479;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:900,0,792
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2248 chr1 96485 . A T 693.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.292;DP=44;Dels=0.00;FS=2.672;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=0.141;QD=15.77;ReadPosRankSum=0.987;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T806|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_96455_96617) GT:AD:DP:GQ:PL 0/1:23,21:44:99:722,0,775
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2249 chr1 96530 . G A 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.281;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.746;QD=18.04;ReadPosRankSum=0.526;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N791|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_96455_96617) GT:AD:DP:GQ:PL 0/1:19,24:43:99:804,0,602
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2250 chr1 96637 . G A 712.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.969;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=0.628;QD=15.17;ReadPosRankSum=-1.798;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:741,0,788
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2251 chr1 96789 . C T 1079.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.380;DP=69;Dels=0.00;FS=0.918;HaplotypeScore=2.8662;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=1;MQRankSum=0.417;QD=15.65;ReadPosRankSum=1.436;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,33:69:99:1108,0,1126
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2252 chr1 96791 . T C 1028.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.571;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=2.8662;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=1;MQRankSum=1.110;QD=15.59;ReadPosRankSum=1.543;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,31:66:99:1057,0,1086
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2253 chr1 96809 . C T 2747.77 . AC=2;AF=1.00;AN=2;DP=70;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.14;MQ0=1;QD=26.52;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,70:70:99:2776,205,0
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2254 chr1 96822 . T G 1272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=73;Dels=0.00;FS=1.969;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=1;MQRankSum=-0.475;QD=17.44;ReadPosRankSum=-0.328;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,40:73:99:1301,0,1128
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2255 chr1 96868 . A T 1270.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.180;DP=72;Dels=0.00;FS=7.826;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=0.620;QD=17.65;ReadPosRankSum=0.631;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,37:72:99:1299,0,1177
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2256 chr1 96880 . C T 1144.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.650;DP=65;Dels=0.00;FS=3.414;HaplotypeScore=12.9967;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=0.795;QD=17.61;ReadPosRankSum=-0.729;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,34:65:99:1173,0,1062
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2257 chr1 96881 . G A 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.233;DP=62;Dels=0.00;FS=4.010;HaplotypeScore=12.9967;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=0.752;QD=8.00;ReadPosRankSum=0.101;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,18:62:99:524,0,1555
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2258 chr1 96885 . G T 1016.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=59;Dels=0.00;FS=2.212;HaplotypeScore=11.9973;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.053;QD=17.23;ReadPosRankSum=-0.675;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1045,0,994
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2259 chr1 97080 . A G 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.185;DP=53;Dels=0.00;FS=3.844;HaplotypeScore=4.8660;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.312;QD=15.58;ReadPosRankSum=-1.630;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L759S|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97071_97171) GT:AD:DP:GQ:PL 0/1:28,25:53:99:854,0,987
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2260 chr1 97141 . G A 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.017;DP=35;Dels=0.00;FS=7.260;HaplotypeScore=3.5776;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.183;QD=19.31;ReadPosRankSum=2.450;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P739S|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97071_97171) GT:AD:DP:GQ:PL 0/1:15,20:35:99:704,0,461
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2261 chr1 97145 . G A 757.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.560;DP=37;Dels=0.00;FS=2.995;HaplotypeScore=5.4724;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.461;QD=20.48;ReadPosRankSum=1.021;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P737|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97071_97171) GT:AD:DP:GQ:PL 0/1:13,23:37:99:786,0,395
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2262 chr1 97223 . A C 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.926;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=2.9971;MLEAC=1;MLEAF=0.500;MQ=58.46;MQ0=0;MQRankSum=0.412;QD=14.31;ReadPosRankSum=0.443;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,28:58:99:858,0,1018
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2263 chr1 97268 . G T 803.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.938;DP=63;Dels=0.00;FS=2.132;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-1.326;QD=12.76;ReadPosRankSum=-0.646;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,27:63:99:832,0,1288
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2264 chr1 97299 . A G 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.601;DP=62;Dels=0.00;FS=0.979;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=1.648;QD=14.48;ReadPosRankSum=-0.290;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,28:62:99:926,0,1199
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2265 chr1 97312 . A G 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.498;DP=67;Dels=0.00;FS=0.988;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=1.608;QD=13.74;ReadPosRankSum=1.761;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:39,28:67:99:949,0,1344
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2266 chr1 97491 . T G 2512.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=1.7219;MLEAC=2;MLEAF=1.00;MQ=59.81;MQ0=0;QD=30.80;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2541,193,0
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2267 chr1 97631 . G C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.243;DP=55;Dels=0.00;FS=2.478;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.377;QD=11.76;ReadPosRankSum=-0.320;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gGt|A723G|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97615_97666) GT:AD:DP:GQ:PL 0/1:34,21:55:99:675,0,1153
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2268 chr1 97696 . C T 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.902;DP=46;Dels=0.00;FS=1.139;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.101;QD=12.26;ReadPosRankSum=1.362;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,18:46:99:592,0,888
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2269 chr1 97749 . C T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.914;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.748;QD=13.02;ReadPosRankSum=-0.831;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:653,0,801
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2270 chr1 97919 . A T 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.901;DP=46;Dels=0.00;FS=4.288;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.066;QD=16.41;ReadPosRankSum=-0.945;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:783,0,771
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2271 chr1 97946 . C G 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.771;DP=41;Dels=0.00;FS=2.814;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=0.879;QD=14.68;ReadPosRankSum=-1.799;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,20:41:99:630,0,670
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2272 chr1 98038 . A G 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.277;DP=50;Dels=0.00;FS=1.115;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.019;QD=17.68;ReadPosRankSum=0.564;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,27:50:99:912,0,770
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2273 chr1 98051 . A T 1890.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.39;MQ0=0;QD=31.05;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1919,144,0
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2274 chr1 98140 . A G 1419.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=31.65;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1448,108,0
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2275 chr1 98179 . G T 887.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.164;DP=54;Dels=0.00;FS=3.840;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-1.099;QD=16.44;ReadPosRankSum=1.013;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,28:54:99:916,0,864
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2276 chr1 98231 . T A 2348.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.96;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2377,178,0
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2277 chr1 98270 . A T 2354.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=28.54;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2383,178,0
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2278 chr1 98294 . A G 790.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=52;Dels=0.00;FS=8.574;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=-1.000;QD=15.21;ReadPosRankSum=0.707;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:819,0,922
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2279 chr1 98466 . A G 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.245;DP=47;Dels=0.00;FS=4.301;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.607;QD=15.61;ReadPosRankSum=-2.224;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:762,0,808
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2280 chr1 98495 . G A 994.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=51;Dels=0.00;FS=4.035;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=0.390;QD=19.51;ReadPosRankSum=-1.113;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,29:51:99:1023,0,696
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2281 chr1 98562 . A C 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.316;DP=55;Dels=0.00;FS=5.711;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-1.698;QD=12.67;ReadPosRankSum=-0.572;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:725,0,1123
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2282 chr1 98613 . T C 586.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.011;DP=41;Dels=0.00;FS=4.457;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.327;QD=14.31;ReadPosRankSum=1.011;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:615,0,801
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2283 chr1 98666 . A T 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.742;DP=47;Dels=0.00;FS=2.744;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=1.116;QD=18.97;ReadPosRankSum=-3.002;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,28:47:99:920,0,631
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2284 chr1 98933 . A T 1037.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.557;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=1;MQRankSum=-0.034;QD=16.22;ReadPosRankSum=0.612;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,33:64:99:1066,0,1072
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2285 chr1 99114 . A T 730.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.229;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-1.092;QD=14.05;ReadPosRankSum=-1.037;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atA|I608|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:28,24:52:99:759,0,894
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2286 chr1 99351 . A T 536.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=45;Dels=0.00;FS=2.527;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-0.683;QD=11.93;ReadPosRankSum=0.637;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctA|L529|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:27,18:45:99:565,0,935
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2287 chr1 99567 . T G 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.874;DP=49;Dels=0.00;FS=12.036;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=57.79;MQ0=0;MQRankSum=0.412;QD=14.02;ReadPosRankSum=-0.533;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaC|E457D|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:27,22:49:99:715,0,877
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2288 chr1 99633 . A G 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.770;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.9944;MLEAC=1;MLEAF=0.500;MQ=58.04;MQ0=0;MQRankSum=1.259;QD=13.09;ReadPosRankSum=-0.599;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S435|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:24,19:43:99:591,0,731
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2289 chr1 99642 . C T 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.111;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=-0.702;QD=11.25;ReadPosRankSum=-0.579;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V432|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:25,18:43:99:512,0,818
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2290 chr1 99729 . G A 977.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.652;DP=53;Dels=0.00;FS=3.841;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.298;QD=18.45;ReadPosRankSum=-1.670;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G403|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:22,31:53:99:1006,0,723
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2291 chr1 99861 . A G 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.654;DP=48;Dels=0.00;FS=2.555;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.822;QD=18.89;ReadPosRankSum=-1.581;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S359|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:19,29:48:99:935,0,572
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2292 chr1 100026 . T C 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=-0.156;QD=20.77;ReadPosRankSum=-0.440;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:14,26:40:99:859,0,407
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2293 chr1 100458 . A C 2457.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.83;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F240L|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_100334_100464) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2486,187,0
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2294 chr1 100484 . A C 2630.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.86;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2659,199,0
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2295 chr1 100660 . T C 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.498;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.981;QD=10.20;ReadPosRankSum=1.005;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:569,0,1225
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2296 chr1 100710 . A C 954.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.633;DP=58;Dels=0.00;FS=1.023;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.213;QD=16.46;ReadPosRankSum=-1.944;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F235C|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_100701_100860) GT:AD:DP:GQ:PL 0/1:29,29:58:99:983,0,1001
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2297 chr1 100778 . A T 1005.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.399;DP=60;Dels=0.00;FS=2.120;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.139;QD=16.76;ReadPosRankSum=0.888;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A212|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_100701_100860) GT:AD:DP:GQ:PL 0/1:29,31:60:99:1034,0,964
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2298 chr1 100875 . C A 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.419;DP=46;Dels=0.00;FS=1.178;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.963;QD=14.84;ReadPosRankSum=-0.794;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,21:46:99:711,0,861
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2299 chr1 100917 . T C 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.969;DP=54;Dels=0.00;FS=3.266;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.189;QD=3.81;ReadPosRankSum=-3.129;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,10:54:99:234,0,1538
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2300 chr1 101397 . A G 870.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.525;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=1;MQRankSum=0.492;QD=15.28;ReadPosRankSum=-0.361;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:899,0,799
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2301 chr1 101547 . A G 1032.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=65;Dels=0.00;FS=10.521;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=0.833;QD=15.89;ReadPosRankSum=-0.151;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,33:65:99:1061,0,1064
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2302 chr1 101623 . T C 2368.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=2;MLEAF=1.00;MQ=59.18;MQ0=0;QD=24.90;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2397,181,0
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2303 chr1 101683 . C T 508.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.992;DP=41;Dels=0.00;FS=9.282;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.040;QD=12.41;ReadPosRankSum=0.437;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:537,0,822
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2304 chr1 101684 . A G 505.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.439;DP=38;Dels=0.00;FS=9.942;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.910;QD=13.31;ReadPosRankSum=-0.411;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:534,0,741
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2305 chr1 101745 . G A 861.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.536;DP=56;Dels=0.00;FS=3.757;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.107;QD=15.39;ReadPosRankSum=0.715;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:890,0,1039
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2306 chr1 101797 . C A 1078.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.276;DP=66;Dels=0.00;FS=0.940;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.032;QD=16.34;ReadPosRankSum=-0.494;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,32:66:99:1107,0,1179
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2307 chr1 101798 . C T 1122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.342;DP=69;Dels=0.00;FS=1.986;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.198;QD=16.27;ReadPosRankSum=-0.582;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,34:69:99:1151,0,1212
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2308 chr1 101823 . C T 2664.77 . AC=2;AF=1.00;AN=2;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=59.92;MQ0=0;QD=30.40;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,69:69:99:2693,202,0
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2309 chr1 101901 . C T 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.165;DP=38;Dels=0.00;FS=6.942;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.22;MQ0=0;MQRankSum=-1.407;QD=20.49;ReadPosRankSum=1.165;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:807,0,440
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2310 chr1 101928 . T A 1680.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=58.67;MQ0=0;QD=38.41;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1709,129,0
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2311 chr1 101943 . G C 988.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.433;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=-1.144;QD=21.97;ReadPosRankSum=-0.445;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,30:45:99:1017,0,464
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2312 chr1 101964 . A T 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.651;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.379;QD=14.30;ReadPosRankSum=-0.037;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,19:43:99:643,0,818
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2313 chr1 102084 . T C 1022.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.787;DP=61;Dels=0.00;FS=0.974;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=-0.816;QD=16.77;ReadPosRankSum=0.440;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,32:61:99:1051,0,930
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2314 chr1 102113 . A C 831.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.327;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=1;MQRankSum=-1.220;QD=15.40;ReadPosRankSum=0.579;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,29:54:99:860,0,828
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2315 chr1 102117 . C A 816.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.320;DP=55;Dels=0.00;FS=2.323;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.48;MQ0=1;MQRankSum=-1.307;QD=14.85;ReadPosRankSum=1.030;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:845,0,861
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2316 chr1 102158 . T C 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.078;DP=54;Dels=0.00;FS=2.323;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=1;MQRankSum=1.951;QD=15.22;ReadPosRankSum=0.526;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,25:54:99:850,0,846
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2317 chr1 102167 . G A 945.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.824;DP=57;Dels=0.00;FS=5.494;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=2;MQRankSum=0.806;QD=16.59;ReadPosRankSum=-2.418;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:974,0,828
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2318 chr1 102180 . T A 2213.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.72;MQ0=2;QD=25.80;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2242,166,0
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2319 chr1 102205 . T C 914.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.548;DP=59;Dels=0.00;FS=1.030;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.23;MQ0=1;MQRankSum=-0.661;QD=15.50;ReadPosRankSum=0.770;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:943,0,978
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2320 chr1 102214 . G C 902.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.037;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.23;MQ0=1;MQRankSum=-2.208;QD=15.30;ReadPosRankSum=-1.135;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:931,0,1005
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2321 chr1 102348 . T G 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.766;DP=44;Dels=0.00;FS=11.766;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.295;QD=18.20;ReadPosRankSum=-0.554;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:829,0,650
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2322 chr1 102411 . T A 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.145;DP=43;Dels=0.00;FS=2.999;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=-0.308;QD=18.02;ReadPosRankSum=-0.382;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:803,0,602
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2323 chr1 102443 . C T 1665.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=69.5886;MLEAC=2;MLEAF=1.00;MQ=58.97;MQ0=0;QD=30.29;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1694,126,0
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2324 chr1 102454 . T A 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.682;DP=46;Dels=0.00;FS=19.456;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=1.572;QD=16.93;ReadPosRankSum=-1.352;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,24:46:99:807,0,705
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2325 chr1 102506 . A G 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.117;DP=36;Dels=0.00;FS=5.231;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=1;MQRankSum=-1.950;QD=17.69;ReadPosRankSum=0.317;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,21:36:99:665,0,522
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2326 chr1 102514 . T C 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.939;DP=39;Dels=0.00;FS=7.216;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=1;MQRankSum=0.617;QD=14.10;ReadPosRankSum=-0.264;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:578,0,741
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2327 chr1 102576 . C G 1795.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.71;MQ0=2;QD=31.84;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1824,135,0
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2328 chr1 102597 . T A 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.154;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=1;MQRankSum=-0.495;QD=17.25;ReadPosRankSum=1.374;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,25:47:99:839,0,693
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2329 chr1 102632 . G A 1747.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.58;MQ0=1;QD=31.12;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1776,135,0
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2330 chr1 102685 . T C 739.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.949;DP=48;Dels=0.00;FS=11.229;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=-2.270;QD=15.41;ReadPosRankSum=-0.310;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:768,0,789
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2331 chr1 102745 . G A 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.203;DP=57;Dels=0.00;FS=1.037;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=-0.626;QD=12.54;ReadPosRankSum=0.203;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,23:57:99:743,0,1192
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2332 chr1 102828 . T A 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.030;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.556;QD=13.44;ReadPosRankSum=-1.748;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:687,0,969
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2333 chr1 102840 . C T 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.773;DP=49;Dels=0.00;FS=2.600;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.317;QD=11.49;ReadPosRankSum=-0.425;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:591,0,1069
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2334 chr1 102853 . A T 1069.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.453;DP=51;Dels=0.00;FS=4.012;HaplotypeScore=1.9978;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.453;QD=20.98;ReadPosRankSum=0.473;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1098,0,644
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2335 chr1 103138 . A T 1021.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=57;Dels=0.00;FS=3.801;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=2;MQRankSum=1.010;QD=17.93;ReadPosRankSum=-0.653;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1050,0,812
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2336 chr1 103150 . T C 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.538;DP=53;Dels=0.00;FS=2.466;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=2;MQRankSum=0.274;QD=14.58;ReadPosRankSum=-0.632;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:801,0,943
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2337 chr1 103189 . A G 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.202;DP=55;Dels=0.00;FS=4.291;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=1;MQRankSum=0.854;QD=12.70;ReadPosRankSum=1.329;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:727,0,1140
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2338 chr1 103225 . G A 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.322;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=1;MQRankSum=1.023;QD=15.72;ReadPosRankSum=-2.002;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,26:54:99:877,0,949
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2339 chr1 103405 . C T 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.168;DP=57;Dels=0.00;FS=2.315;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=0.280;QD=17.24;ReadPosRankSum=1.223;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,30:57:99:1011,0,920
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2340 chr1 103515 . G A 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.131;DP=49;Dels=0.00;FS=2.536;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.222;QD=13.79;ReadPosRankSum=-0.778;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:704,0,944
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2341 chr1 103542 . G C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.229;DP=44;Dels=0.00;FS=2.800;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.991;QD=19.31;ReadPosRankSum=-1.492;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,26:44:99:878,0,558
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2342 chr1 103599 . C G 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.605;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=2.7842;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.583;QD=15.71;ReadPosRankSum=0.473;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,22:46:99:751,0,773
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2343 chr1 103609 . A C 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.351;DP=48;Dels=0.00;FS=4.201;HaplotypeScore=3.7837;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.330;QD=16.89;ReadPosRankSum=-1.218;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:839,0,793
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2344 chr1 103612 . C T 847.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.050;DP=49;Dels=0.00;FS=1.101;HaplotypeScore=3.7837;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.130;QD=17.30;ReadPosRankSum=-1.410;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:876,0,826
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2345 chr1 103621 . G T 902.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.198;QD=17.70;ReadPosRankSum=-1.915;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:931,0,802
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2346 chr1 103691 . C A 1271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.171;DP=60;Dels=0.00;FS=2.252;HaplotypeScore=1.9982;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-0.061;QD=21.20;ReadPosRankSum=2.646;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,37:60:99:1300,0,754
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2347 chr1 103828 . C G 947.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.716;DP=55;Dels=0.00;FS=7.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=0.227;QD=17.23;ReadPosRankSum=-0.109;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:976,0,894
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2348 chr1 103856 . C T 588.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.458;DP=49;Dels=0.00;FS=16.948;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=60.22;MQ0=0;MQRankSum=-1.149;QD=12.02;ReadPosRankSum=-0.254;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,20:49:99:617,0,1000
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2349 chr1 103995 . G A 806.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.761;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=-0.440;QD=12.81;ReadPosRankSum=-0.510;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,26:63:99:835,0,1325
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2350 chr1 104120 . C G 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.402;DP=54;Dels=0.00;FS=5.785;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-0.227;QD=12.09;ReadPosRankSum=-1.032;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:681,0,1040
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2351 chr1 104149 . G A 983.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.565;DP=51;Dels=0.00;FS=2.555;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=-0.048;QD=19.29;ReadPosRankSum=-0.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,30:51:99:1012,0,605
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2352 chr1 104155 . A G 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.401;DP=49;Dels=0.00;FS=4.412;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=0.798;QD=10.73;ReadPosRankSum=2.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,17:49:99:554,0,1041
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|
|
2353 chr1 104159 . C T 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.146;DP=51;Dels=0.00;FS=4.244;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.89;MQ0=0;MQRankSum=-1.120;QD=11.25;ReadPosRankSum=1.685;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,19:51:99:602,0,1079
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|
|
2354 chr1 104167 . T C 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.897;DP=51;Dels=0.00;FS=2.473;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-1.109;QD=12.25;ReadPosRankSum=1.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,20:51:99:653,0,1056
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|
|
2355 chr1 104213 . C T 727.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.709;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.104;QD=13.73;ReadPosRankSum=-1.481;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:756,0,1034
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|
|
2356 chr1 104372 . G A 2025.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9914;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2054,156,0
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|
|
2357 chr1 104376 . T C 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.581;DP=53;Dels=0.00;FS=10.088;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.367;QD=18.28;ReadPosRankSum=-1.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,29:53:99:997,0,714
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|
|
2358 chr1 104545 . A C 1079.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.282;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.847;QD=17.70;ReadPosRankSum=-0.007;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1108,0,937
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|
|
2359 chr1 104549 . C A 2426.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2455,184,0
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|
|
2360 chr1 104570 . G T 1119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.314;DP=66;Dels=0.00;FS=2.084;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.212;QD=16.97;ReadPosRankSum=0.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,34:66:99:1148,0,1049
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|
|
2361 chr1 104631 . T A 1016.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.341;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=2.7461;MLEAC=1;MLEAF=0.500;MQ=60.16;MQ0=0;MQRankSum=-1.676;QD=15.18;ReadPosRankSum=-0.596;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,32:67:99:1045,0,1181
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|
|
2362 chr1 104738 . A T 1287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.183;DP=70;Dels=0.00;FS=10.396;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.242;QD=18.40;ReadPosRankSum=0.383;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,38:70:99:1316,0,1019
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|
|
2363 chr1 104775 . C A 1237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.775;DP=61;Dels=0.00;FS=2.287;HaplotypeScore=1.8663;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=1.380;QD=20.29;ReadPosRankSum=0.229;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,37:61:99:1266,0,700
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|
|
2364 chr1 104901 . T G 991.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.076;DP=55;Dels=0.00;FS=2.401;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.582;QD=18.03;ReadPosRankSum=0.464;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:1020,0,851
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|
|
2365 chr1 104914 . G C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.756;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.187;QD=15.35;ReadPosRankSum=-0.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,26:54:99:857,0,929
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|
|
2366 chr1 105215 . A G 1426.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.23;MQ0=0;QD=27.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1455,111,0
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|
|
2367 chr1 105276 . A G 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.843;DP=49;Dels=0.02;FS=1.174;HaplotypeScore=2.9659;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=-0.120;QD=20.71;ReadPosRankSum=0.930;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,29:48:99:1043,0,542
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|
|
2368 chr1 105289 . C A 1056.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.027;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=1;MQRankSum=0.027;QD=19.57;ReadPosRankSum=0.587;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,31:54:99:1085,0,685
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|
2369 chr1 105333 . G A 2241.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=1;QD=30.11;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2270,169,0
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|
|
2370 chr1 105363 . G A 2110.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=1;QD=30.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2139,160,0
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|
2371 chr1 105391 . A G 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.194;DP=59;Dels=0.00;FS=7.470;HaplotypeScore=3.5213;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.039;QD=12.00;ReadPosRankSum=-0.723;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,23:59:99:736,0,1250
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2372 chr1 105594 . A G 2739.77 . AC=2;AF=1.00;AN=2;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=3.2358;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;QD=31.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,74:74:99:2768,214,0
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|
|
2373 chr1 105636 . C T 1107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.014;DP=70;Dels=0.00;FS=8.071;HaplotypeScore=4.6697;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.786;QD=15.83;ReadPosRankSum=0.090;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,34:70:99:1136,0,1128
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|
2374 chr1 105656 . G A 984.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.247;DP=63;Dels=0.00;FS=6.709;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-1.218;QD=15.63;ReadPosRankSum=-0.697;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,33:63:99:1013,0,1033
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|
2375 chr1 105661 . T A 1957.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.41;MQ0=0;QD=36.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:1986,147,0
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|
2376 chr1 105662 . T A 2023.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.43;MQ0=0;QD=25.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2052,153,0
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|
2377 chr1 105733 . T G 2248.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.503;DP=62;Dels=0.00;FS=3.153;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.75;MQ0=0;MQRankSum=0.335;QD=30.29;ReadPosRankSum=1.565;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:1,61:62:99:2277,135,0
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|
2378 chr1 105750 . C T 2320.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.75;MQ0=0;QD=27.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2349,175,0
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|
|
2379 chr1 105769 . C G 923.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.899;DP=68;Dels=0.00;FS=3.397;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.071;QD=13.58;ReadPosRankSum=1.453;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,31:68:99:952,0,1291
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|
2380 chr1 105775 . A G 1185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.270;DP=66;Dels=0.00;FS=3.451;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=2.634;QD=17.97;ReadPosRankSum=-0.899;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1214,0,951
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|
2381 chr1 105776 . C T 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.385;DP=66;Dels=0.00;FS=3.451;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-1.105;QD=13.42;ReadPosRankSum=0.822;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,31:66:99:914,0,1186
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2382 chr1 105815 . C A 1124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.954;DP=65;Dels=0.00;FS=2.177;HaplotypeScore=2.3346;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=0.388;QD=17.30;ReadPosRankSum=-1.112;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,35:65:99:1153,0,982
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|
2383 chr1 105914 . A G 985.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.125;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.402;QD=19.33;ReadPosRankSum=1.939;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1014,0,607
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|
2384 chr1 105940 . A G 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.169;DP=55;Dels=0.00;FS=1.036;HaplotypeScore=6.1984;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.580;QD=11.83;ReadPosRankSum=1.117;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:34,21:55:99:679,0,1160
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|
2385 chr1 106000 . G A 723.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.619;DP=48;Dels=0.00;FS=2.471;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.475;QD=15.08;ReadPosRankSum=-0.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:25,23:48:99:752,0,840
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|
2386 chr1 106003 . C T 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.610;DP=49;Dels=0.00;FS=2.512;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.730;QD=15.87;ReadPosRankSum=-0.650;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:25,24:49:99:806,0,839
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|
2387 chr1 106222 . A T 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.445;DP=56;Dels=0.00;FS=3.858;HaplotypeScore=2.9889;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-0.294;QD=10.64;ReadPosRankSum=-1.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:34,22:56:99:624,0,1107
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|
2388 chr1 106301 . G A 1226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.629;DP=76;Dels=0.00;FS=3.172;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.14;MQ0=0;MQRankSum=0.057;QD=16.14;ReadPosRankSum=-0.161;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:38,38:76:99:1255,0,1277
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|
|
2389 chr1 106304 . C T 1117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.244;DP=75;Dels=0.00;FS=3.136;HaplotypeScore=1.6988;MLEAC=1;MLEAF=0.500;MQ=60.14;MQ0=0;MQRankSum=0.178;QD=14.90;ReadPosRankSum=0.871;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:38,36:75:99:1146,0,1287
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|
2390 chr1 106352 . T A 2717.77 . AC=2;AF=1.00;AN=2;DP=70;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.81;MQ0=0;QD=31.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 1/1:0,70:70:99:2746,208,0
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|
|
2391 chr1 106447 . C A 879.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.452;DP=58;Dels=0.00;FS=3.667;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=1.169;QD=15.17;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:908,0,1064
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|
2392 chr1 106476 . T G 1349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.697;DP=77;Dels=0.00;FS=16.431;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=1.137;QD=17.53;ReadPosRankSum=2.024;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,40:77:99:1378,0,1148
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2393 chr1 106481 . T C 939.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.295;DP=76;Dels=0.00;FS=14.274;HaplotypeScore=3.8312;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=0.091;QD=12.37;ReadPosRankSum=-0.562;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,32:76:99:968,0,1489
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2394 chr1 106482 . G A 959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.300;DP=76;Dels=0.00;FS=17.089;HaplotypeScore=2.8316;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-2.404;QD=12.63;ReadPosRankSum=0.132;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,32:76:99:988,0,1538
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2395 chr1 106502 . C T 1216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.575;DP=80;Dels=0.00;FS=9.385;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-0.833;QD=15.21;ReadPosRankSum=0.949;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,38:80:99:1245,0,1351
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2396 chr1 106522 . G C 1262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.345;DP=73;Dels=0.00;FS=7.905;HaplotypeScore=3.1224;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=-0.745;QD=17.30;ReadPosRankSum=0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,37:73:99:1291,0,1178
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2397 chr1 106546 . A T 1107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.761;DP=68;Dels=0.00;FS=21.595;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.577;QD=16.29;ReadPosRankSum=0.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,35:68:99:1136,0,1064
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2398 chr1 106547 . T A 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.040;DP=65;Dels=0.00;FS=19.861;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.581;QD=13.38;ReadPosRankSum=0.754;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,32:65:99:898,0,1081
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2399 chr1 106583 . A C 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.634;DP=51;Dels=0.00;FS=1.066;HaplotypeScore=1.8313;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.161;QD=18.17;ReadPosRankSum=-1.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:955,0,750
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2400 chr1 106636 . C G 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.551;DP=53;Dels=0.00;FS=4.175;HaplotypeScore=2.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.208;QD=12.96;ReadPosRankSum=0.713;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:715,0,996
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2401 chr1 106713 . G T 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.015;DP=52;Dels=0.00;FS=10.628;HaplotypeScore=24.7277;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-1.007;QD=15.17;ReadPosRankSum=0.623;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:817,0,902
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2402 chr1 106753 . T A 10.2 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.249;DP=40;Dels=0.00;FS=2.183;HaplotypeScore=19.7108;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=0.900;QD=0.26;ReadPosRankSum=-1.963;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,5:40:38:38,0,1284
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2403 chr1 106797 . G A 1867.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1896,141,0
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2404 chr1 106811 . G A,C 1402.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;QD=32.61;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/2:0,27,16:43:99:1616,598,517,1018,0,970
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2405 chr1 106817 . C T 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.837;DP=40;Dels=0.00;FS=2.928;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.801;QD=23.29;ReadPosRankSum=0.241;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:14,26:40:99:960,0,454
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2406 chr1 106840 . C T 1108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.900;DP=44;Dels=0.00;FS=2.926;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.801;QD=25.20;ReadPosRankSum=1.029;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:13,31:44:99:1137,0,394
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2407 chr1 106843 . G C 355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.852;DP=44;Dels=0.00;FS=2.926;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.206;QD=8.09;ReadPosRankSum=-1.260;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:384,0,1140
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2408 chr1 106856 . G A 1422.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.48;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1451,108,0
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2409 chr1 106885 . A T 744.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.646;QD=22.57;ReadPosRankSum=0.921;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:10,23:33:99:773,0,304
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2410 chr1 106934 . T A 450.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.70;MQ0=0;QD=34.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,13:13:36:479,36,0
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2411 chr1 106992 . T C 120.03 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.08;MQ0=3;QD=15.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:3,5:8:12:148,12,0
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2412 chr1 106996 . C T 120.03 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.08;MQ0=3;QD=15.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:3,5:8:12:148,12,0
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2413 chr1 107014 . C T 121.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.88;MQ0=2;QD=17.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:1,6:7:12:149,12,0
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2414 chr1 107015 . T C 121.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.11;MQ0=1;QD=20.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:1,5:6:12:149,12,0
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2415 chr1 107020 . C T 121.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.11;MQ0=1;QD=20.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,5:6:12:149,12,0
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2416 chr1 107021 . T C 121.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.11;MQ0=1;QD=20.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,6:6:12:149,12,0
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2417 chr1 107045 . G A 121.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.88;MQ0=2;QD=17.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:2,5:7:12:149,12,0
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2418 chr1 107068 . G A 83.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.13;MQ0=1;QD=16.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:111,9,0
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2419 chr1 107156 . A T 10.9 LowQual AC=2;AF=1.00;AN=2;BaseQRankSum=0.736;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.26;MQ0=3;MQRankSum=0.736;QD=1.82;ReadPosRankSum=-0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:4,2:6:3:37,3,0
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2420 chr1 107197 . C T 120.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.887;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.4725;MLEAC=2;MLEAF=1.00;MQ=12.97;MQ0=14;MQRankSum=2.957;QD=3.75;ReadPosRankSum=1.774;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:27,5:32:12:148,12,0
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2421 chr1 107202 . G A 116.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.449;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.5362;MLEAC=2;MLEAF=1.00;MQ=13.15;MQ0=13;MQRankSum=2.654;QD=3.63;ReadPosRankSum=1.674;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:18,14:32:12:144,12,0
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2422 chr1 107216 . G T 87.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.623;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=2.1146;MLEAC=2;MLEAF=1.00;MQ=12.19;MQ0=12;MQRankSum=1.535;QD=2.73;ReadPosRankSum=0.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:19,6:32:9:115,9,0
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2423 chr1 107223 . G A 78.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.529;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=3.0304;MLEAC=2;MLEAF=1.00;MQ=12.37;MQ0=12;MQRankSum=2.646;QD=2.45;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:27,5:32:9:106,9,0
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2424 chr1 107234 . T C 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.256;DP=34;Dels=0.00;FS=10.000;HaplotypeScore=3.3679;MLEAC=1;MLEAF=0.500;MQ=15.56;MQ0=13;MQRankSum=2.161;QD=1.99;ReadPosRankSum=-0.955;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,4:34:58:96,0,58
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2425 chr1 107332 . A G 264.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.49;MQ0=1;QD=24.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,10:11:24:293,24,0
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2426 chr1 107410 . T G 122.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.550;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.88;MQ0=4;MQRankSum=1.754;QD=11.09;ReadPosRankSum=-1.754;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:7,4:11:12:150,12,0
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2427 chr1 107457 . G A 251.8 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.263;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=1.9157;MLEAC=2;MLEAF=1.00;MQ=19.81;MQ0=12;MQRankSum=3.308;QD=8.99;ReadPosRankSum=0.368;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:20,8:28:21:280,21,0
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2428 chr1 107475 . G T 273.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.088;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.53;MQ0=12;MQRankSum=3.532;QD=9.13;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:19,9:30:24:302,24,0
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|
2429 chr1 107492 . A G 271.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.144;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.9159;MLEAC=2;MLEAF=1.00;MQ=19.86;MQ0=12;MQRankSum=3.416;QD=9.37;ReadPosRankSum=0.722;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:20,9:29:24:300,24,0
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|
2430 chr1 107493 . A C 268.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.847;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.8490;MLEAC=2;MLEAF=1.00;MQ=19.86;MQ0=12;MQRankSum=3.281;QD=9.27;ReadPosRankSum=0.318;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:18,9:29:24:297,24,0
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|
2431 chr1 107755 . G A 128.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.00;MQ0=0;QD=32.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:156,12,0
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|
2432 chr1 107795 . G T 489.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.82;MQ0=1;QD=34.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,14:14:39:518,39,0
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|
|
2433 chr1 107900 . T C 502.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.86;MQ0=0;QD=33.52;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,15:15:42:531,42,0
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|
|
2434 chr1 107903 . A G 489.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.86;MQ0=0;QD=32.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,15:15:42:518,42,0
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|
|
2435 chr1 108008 . A T 911.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.22;MQ0=0;QD=25.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,26:26:72:940,72,0
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|
|
2436 chr1 108057 . A G 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.271;DP=45;Dels=0.00;FS=1.181;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.59;MQ0=1;MQRankSum=2.204;QD=13.15;ReadPosRankSum=3.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:620,0,784
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|
|
2437 chr1 108058 . C T 789.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.271;DP=45;Dels=0.00;FS=1.167;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.59;MQ0=1;MQRankSum=-1.780;QD=17.55;ReadPosRankSum=-2.817;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:818,0,619
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|
|
2438 chr1 108069 . A G 872.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.51;MQ0=1;QD=25.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,24:24:66:901,66,0
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|
|
2439 chr1 108088 . C T 944.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.22;MQ0=1;QD=29.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:973,72,0
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|
|
2440 chr1 108089 . A G 933.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.22;MQ0=1;QD=32.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:962,72,0
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|
|
2441 chr1 108104 . G A 657.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.287;DP=47;Dels=0.00;FS=1.121;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.48;MQ0=0;MQRankSum=-4.097;QD=14.00;ReadPosRankSum=-5.544;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:686,0,806
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|
|
2442 chr1 108110 . C T 1376.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.31;MQ0=0;QD=34.42;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1405,114,0
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|
|
2443 chr1 108111 . A G 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.553;DP=40;Dels=0.00;FS=1.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.31;MQ0=0;MQRankSum=2.878;QD=9.97;ReadPosRankSum=4.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,14:40:99:427,0,745
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|
|
2444 chr1 108112 . G A 397.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.496;DP=40;Dels=0.00;FS=1.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.31;MQ0=0;MQRankSum=2.793;QD=9.94;ReadPosRankSum=4.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,14:40:99:426,0,750
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|
|
2445 chr1 108120 . A C 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=48;Dels=0.00;FS=2.509;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.28;MQ0=0;MQRankSum=-2.348;QD=14.56;ReadPosRankSum=0.021;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,27:48:99:727,0,612
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|
|
2446 chr1 108125 . T C 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.178;DP=46;Dels=0.00;FS=2.597;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=33.80;MQ0=0;MQRankSum=1.807;QD=11.10;ReadPosRankSum=-1.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,19:46:99:539,0,755
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|
|
2447 chr1 108127 . C T 1486.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9987;MLEAC=2;MLEAF=1.00;MQ=33.75;MQ0=0;QD=33.04;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1515,126,0
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|
|
2448 chr1 108128 . A G 1489.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9987;MLEAC=2;MLEAF=1.00;MQ=33.75;MQ0=0;QD=33.11;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1518,126,0
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|
|
2449 chr1 108131 . C T 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.573;DP=52;Dels=0.00;FS=5.913;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=31.93;MQ0=3;MQRankSum=-1.012;QD=13.32;ReadPosRankSum=2.875;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:721,0,597
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|
|
2450 chr1 108137 . T A 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.771;DP=52;Dels=0.00;FS=5.913;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=31.93;MQ0=3;MQRankSum=-1.072;QD=13.30;ReadPosRankSum=4.498;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:720,0,593
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|
|
2451 chr1 108138 . G C 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.272;DP=52;Dels=0.00;FS=5.913;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=31.93;MQ0=3;MQRankSum=0.952;QD=10.88;ReadPosRankSum=-4.658;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:594,0,722
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|
2452 chr1 108168 . G A 896.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.18;MQ0=3;QD=25.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,35:35:81:925,81,0
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|
2453 chr1 108170 . A G 268.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.538;DP=35;Dels=0.00;FS=5.449;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.18;MQ0=3;MQRankSum=0.019;QD=7.68;ReadPosRankSum=2.982;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:297,0,467
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|
|
2454 chr1 108172 . A T 271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.052;DP=34;Dels=0.00;FS=5.449;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.06;MQ0=3;MQRankSum=0.020;QD=7.99;ReadPosRankSum=2.918;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:300,0,431
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|
2455 chr1 108179 . A T 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.474;DP=31;Dels=0.00;FS=1.744;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.94;MQ0=3;MQRankSum=-0.092;QD=7.67;ReadPosRankSum=3.271;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:266,0,355
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|
2456 chr1 108237 . T C 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.136;DP=52;Dels=0.00;FS=1.519;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.32;MQ0=1;MQRankSum=0.076;QD=2.84;ReadPosRankSum=-3.358;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,9:51:99:176,0,1420
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|
|
2457 chr1 108244 . C T 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.012;DP=52;Dels=0.00;FS=3.548;HaplotypeScore=34.2618;MLEAC=1;MLEAF=0.500;MQ=45.72;MQ0=1;MQRankSum=0.507;QD=3.19;ReadPosRankSum=-2.533;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,9:52:99:194,0,1435
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|
2458 chr1 108245 . G A 164.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.803;DP=52;Dels=0.00;FS=3.605;HaplotypeScore=34.2618;MLEAC=1;MLEAF=0.500;MQ=45.72;MQ0=1;MQRankSum=0.358;QD=3.17;ReadPosRankSum=-2.508;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,9:52:99:193,0,1432
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|
|
2459 chr1 108320 . T C 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.061;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.89;MQ0=0;MQRankSum=-1.995;QD=13.85;ReadPosRankSum=-0.737;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:804,0,1051
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|
|
2460 chr1 108356 . C A 567.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.305;DP=72;Dels=0.00;FS=1.099;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=1.076;QD=7.89;ReadPosRankSum=-0.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:50,22:72:99:596,0,1658
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|
|
2461 chr1 108358 . G C 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.113;DP=72;Dels=0.00;FS=2.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=0.603;QD=8.11;ReadPosRankSum=-0.180;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:50,22:72:99:612,0,1682
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|
|
2462 chr1 108381 . C G 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.195;DP=57;Dels=0.00;FS=2.406;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=1.583;QD=9.47;ReadPosRankSum=-0.279;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,19:57:99:568,0,1331
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|
|
2463 chr1 108383 . C T 640.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.245;DP=59;Dels=0.00;FS=2.367;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=0.657;QD=10.86;ReadPosRankSum=-0.768;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,21:59:99:669,0,1309
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|
|
2464 chr1 108421 . T C 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.732;DP=54;Dels=0.00;FS=5.922;HaplotypeScore=10.9950;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.455;QD=12.48;ReadPosRankSum=-1.854;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:702,0,1090
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|
|
2465 chr1 108425 . C T 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.158;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=10.9950;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.604;QD=12.76;ReadPosRankSum=0.604;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:666,0,1049
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|
|
2466 chr1 108449 . A G 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.445;DP=52;Dels=0.00;FS=6.027;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=1;MQRankSum=1.139;QD=12.59;ReadPosRankSum=-1.005;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,22:52:99:683,0,1017
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|
|
2467 chr1 108459 . T C 989.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=57;Dels=0.00;FS=9.593;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=1;MQRankSum=-0.379;QD=17.36;ReadPosRankSum=1.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1018,0,841
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|
|
2468 chr1 108471 . G A 2484.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=1;QD=27.75;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,65:65:99:2513,190,0
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|
|
2469 chr1 108482 . T C 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.027;DP=70;Dels=0.00;FS=6.663;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=1;MQRankSum=-0.510;QD=11.90;ReadPosRankSum=-0.092;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,28:70:99:861,0,1470
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|
|
2470 chr1 108528 . T A 1085.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.439;DP=90;Dels=0.00;FS=2.962;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=3;MQRankSum=-0.509;QD=12.06;ReadPosRankSum=-0.057;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:53,37:90:99:1114,0,1842
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|
|
2471 chr1 108603 . T C 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.997;DP=72;Dels=0.00;FS=5.096;HaplotypeScore=1.9946;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-1.165;QD=10.07;ReadPosRankSum=0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:48,24:72:99:753,0,1647
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|
|
2472 chr1 108612 . T C 863.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.430;DP=75;Dels=0.00;FS=7.991;HaplotypeScore=66.7830;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-0.528;QD=11.52;ReadPosRankSum=0.647;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:46,29:75:99:892,0,1572
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|
|
2473 chr1 108628 . A C 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.110;DP=62;Dels=0.00;FS=2.268;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=-0.346;QD=10.00;ReadPosRankSum=1.802;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:40,22:62:99:648,0,1375
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|
|
2474 chr1 108660 . G A 823.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.462;DP=51;Dels=0.00;FS=1.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-0.575;QD=16.15;ReadPosRankSum=-1.008;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:852,0,837
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|
|
2475 chr1 108664 . C T 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.192;DP=49;Dels=0.00;FS=2.568;HaplotypeScore=1.7820;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=-0.551;QD=15.63;ReadPosRankSum=-1.653;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:794,0,758
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|
|
2476 chr1 108691 . A T 981.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:1010,78,0
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|
|
2477 chr1 108698 . C G 520.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.147;DP=38;Dels=0.00;FS=8.656;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.27;MQ0=0;MQRankSum=0.998;QD=13.70;ReadPosRankSum=-4.374;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:549,0,669
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|
|
2478 chr1 108709 . A C 516.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.320;DP=37;Dels=0.00;FS=12.587;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.28;MQ0=0;MQRankSum=0.442;QD=13.97;ReadPosRankSum=-0.411;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:545,0,634
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|
|
2479 chr1 108759 . T A 790.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.087;DP=55;Dels=0.00;FS=33.086;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.45;MQ0=0;MQRankSum=1.155;QD=14.38;ReadPosRankSum=0.868;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:819,0,968
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|
|
2480 chr1 108772 . G A 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.015;DP=54;Dels=0.00;FS=28.588;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-1.120;QD=13.33;ReadPosRankSum=-0.805;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:748,0,1076
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|
|
2481 chr1 108785 . C G 1842.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.64;MQ0=0;QD=29.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,47:48:99:1871,141,0
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|
|
2482 chr1 108796 . C T 1158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.176;DP=42;Dels=0.00;FS=2.508;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.950;QD=27.59;ReadPosRankSum=-0.858;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,33:42:99:1187,0,248
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|
|
2483 chr1 108799 . G A 1078.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.972;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.684;QD=26.97;ReadPosRankSum=-0.583;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,31:40:99:1107,0,249
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|
|
2484 chr1 108827 . C T 383.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.074;DP=32;Dels=0.00;FS=27.227;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=-3.223;QD=11.99;ReadPosRankSum=-0.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,13:32:99:412,0,643
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|
|
2485 chr1 108889 . C T 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.037;DP=18;Dels=0.00;FS=3.214;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=-1.616;QD=26.71;ReadPosRankSum=-1.335;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:2,16:18:33:509,0,33
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|
|
2486 chr1 108893 . A G 636.84 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.770;DP=22;Dels=0.00;FS=3.067;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=-0.400;QD=28.95;ReadPosRankSum=-1.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:2,20:22:18:665,0,18
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|
|
2487 chr1 108940 . T G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.018;DP=35;Dels=0.00;FS=14.801;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.160;QD=22.74;ReadPosRankSum=1.404;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,24:35:99:824,0,345
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|
|
2488 chr1 108944 . A G 1416.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1445,108,0
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|
|
2489 chr1 108956 . G A 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.064;DP=38;Dels=0.00;FS=10.987;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.354;QD=23.86;ReadPosRankSum=-2.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,27:38:99:935,0,334
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|
|
2490 chr1 108987 . G A 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.462;DP=30;Dels=0.00;FS=5.654;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=0.022;QD=9.69;ReadPosRankSum=-0.374;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,10:30:99:319,0,707
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|
|
2491 chr1 108988 . A G,T 817.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=59.21;MQ0=0;QD=31.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/2:0,10,16:26:99:981,597,567,383,0,335
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|
|
2492 chr1 108990 . G A,T 801.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=59.21;MQ0=0;QD=30.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/2:0,10,16:26:99:964,583,553,382,0,333
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|
|
2493 chr1 109006 . G A 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.423;DP=30;Dels=0.00;FS=9.472;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-0.963;QD=18.89;ReadPosRankSum=2.637;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:595,0,411
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|
|
2494 chr1 109022 . A G 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.058;DP=22;Dels=0.00;FS=2.126;HaplotypeScore=3.9974;MLEAC=1;MLEAF=0.500;MQ=58.25;MQ0=0;MQRankSum=-1.672;QD=19.94;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:8,14:22:99:467,0,255
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|
2495 chr1 109058 . A C 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.156;DP=26;Dels=0.00;FS=6.641;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=0;MQRankSum=-4.308;QD=19.07;ReadPosRankSum=0.467;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,15:26:99:524,0,360
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|
2496 chr1 109062 . A G 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.218;DP=27;Dels=0.00;FS=9.864;HaplotypeScore=13.9930;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=0;MQRankSum=-4.440;QD=16.55;ReadPosRankSum=1.626;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,14:27:99:475,0,443
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|
2497 chr1 109083 . T C 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.570;DP=34;Dels=0.00;FS=14.575;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=-3.295;QD=14.64;ReadPosRankSum=2.432;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,16:34:99:526,0,626
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|
2498 chr1 109085 . G A 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.173;DP=37;Dels=0.00;FS=16.965;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=-3.692;QD=15.80;ReadPosRankSum=1.109;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,19:37:99:613,0,599
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|
2499 chr1 109091 . G A 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.910;DP=42;Dels=0.00;FS=18.757;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-1.845;QD=17.92;ReadPosRankSum=-0.379;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:781,0,633
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|
2500 chr1 109097 . T A 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.958;DP=44;Dels=0.00;FS=18.557;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-2.652;QD=15.47;ReadPosRankSum=-1.072;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:709,0,666
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|
2501 chr1 109115 . C T 693.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.704;DP=42;Dels=0.00;FS=9.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=-1.862;QD=16.52;ReadPosRankSum=-1.233;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:722,0,721
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|
2502 chr1 109169 . G C 974.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.259;DP=46;Dels=0.00;FS=1.139;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.191;QD=21.19;ReadPosRankSum=-0.979;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,28:46:99:1003,0,590
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|
2503 chr1 109252 . C T 1130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.266;DP=54;Dels=0.00;FS=7.888;HaplotypeScore=2.6437;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.461;QD=20.94;ReadPosRankSum=-0.763;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,33:54:99:1159,0,672
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|
2504 chr1 109254 . G A 2185.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.6648;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=0;QD=32.54;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2214,166,0
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|
|
2505 chr1 109269 . C T 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.574;DP=54;Dels=0.00;FS=15.735;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=-0.175;QD=11.68;ReadPosRankSum=0.455;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:659,0,1060
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|
2506 chr1 109311 . T A 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.611;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=0.952;QD=14.86;ReadPosRankSum=-0.651;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,26:50:99:771,0,715
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|
|
2507 chr1 109317 . T C 629.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.722;DP=48;Dels=0.00;FS=1.079;HaplotypeScore=2.3119;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=0.702;QD=13.12;ReadPosRankSum=-0.021;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:658,0,763
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|
|
2508 chr1 109405 . T C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.645;DP=42;Dels=0.00;FS=6.930;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=2;MQRankSum=-0.585;QD=15.68;ReadPosRankSum=-0.938;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,24:42:99:687,0,600
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|
|
2509 chr1 109412 . C A 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.217;DP=47;Dels=0.00;FS=6.249;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=2;MQRankSum=1.422;QD=16.31;ReadPosRankSum=-0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:795,0,679
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|
|
2510 chr1 109420 . A T 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.500;DP=50;Dels=0.00;FS=1.145;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=2;MQRankSum=1.148;QD=15.90;ReadPosRankSum=-0.010;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:823,0,754
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|
|
2511 chr1 109464 . C T 986.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.050;DP=60;Dels=0.00;FS=7.465;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.83;MQ0=3;MQRankSum=-1.214;QD=16.45;ReadPosRankSum=-0.217;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1015,0,831
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|
|
2512 chr1 109479 . G A 923.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.708;DP=53;Dels=0.00;FS=8.418;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=3;MQRankSum=2.123;QD=17.43;ReadPosRankSum=-1.356;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,32:53:99:952,0,701
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|
|
2513 chr1 109530 . G A 1926.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9916;MLEAC=2;MLEAF=1.00;MQ=58.84;MQ0=1;QD=29.57;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:1955,147,0
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|
|
2514 chr1 109539 . T C 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.577;DP=51;Dels=0.00;FS=2.465;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=1;MQRankSum=1.378;QD=17.49;ReadPosRankSum=-0.518;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,29:51:99:920,0,726
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|
|
2515 chr1 109549 . C T 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.389;DP=60;Dels=0.00;FS=1.044;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=1;MQRankSum=-0.603;QD=13.80;ReadPosRankSum=0.237;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:856,0,1084
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|
|
2516 chr1 109620 . A T 2529.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.89;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2558,199,0
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|
|
2517 chr1 109646 . G A 941.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.540;DP=57;Dels=0.00;FS=1.029;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-0.471;QD=16.52;ReadPosRankSum=0.311;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:970,0,961
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|
|
2518 chr1 109673 . A T 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.120;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.499;QD=14.44;ReadPosRankSum=1.382;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,28:61:99:909,0,993
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|
|
2519 chr1 109689 . C T 2343.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.70;MQ0=0;QD=36.47;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2372,175,0
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|
|
2520 chr1 109734 . G A 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.181;DP=56;Dels=0.00;FS=2.436;HaplotypeScore=1.7608;MLEAC=1;MLEAF=0.500;MQ=56.24;MQ0=0;MQRankSum=0.033;QD=14.01;ReadPosRankSum=0.115;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:813,0,1012
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|
|
2521 chr1 109767 . C T 725.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.208;DP=54;Dels=0.00;FS=5.623;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=0;MQRankSum=-0.035;QD=13.44;ReadPosRankSum=1.596;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,25:54:99:754,0,928
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|
|
2522 chr1 109788 . T C 240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.340;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.10;MQ0=0;MQRankSum=-3.116;QD=5.73;ReadPosRankSum=2.141;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,10:42:99:269,0,1133
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|
|
2523 chr1 109814 . C T 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.124;DP=47;Dels=0.00;FS=1.192;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=51.18;MQ0=0;MQRankSum=-4.437;QD=10.59;ReadPosRankSum=-1.494;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,18:47:99:526,0,933
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|
|
2524 chr1 109855 . C G 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.579;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=4.1986;MLEAC=1;MLEAF=0.500;MQ=53.14;MQ0=0;MQRankSum=-5.305;QD=11.95;ReadPosRankSum=1.686;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:542,0,816
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|
|
2525 chr1 109898 . G A 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.567;DP=42;Dels=0.00;FS=4.504;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.07;MQ0=0;MQRankSum=-4.596;QD=14.49;ReadPosRankSum=-0.038;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:637,0,754
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|
|
2526 chr1 109948 . G A 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.655;DP=45;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.56;MQ0=0;MQRankSum=-4.171;QD=13.66;ReadPosRankSum=-0.931;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,26:45:99:643,0,655
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|
|
2527 chr1 109992 . C G 1090.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=20.2910;MLEAC=2;MLEAF=1.00;MQ=38.79;MQ0=0;QD=25.97;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,42:42:90:1119,90,0
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|
|
2528 chr1 110000 . T C 301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.991;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=3.3547;MLEAC=1;MLEAF=0.500;MQ=40.16;MQ0=0;MQRankSum=-3.699;QD=6.42;ReadPosRankSum=0.672;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:330,0,703
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|
|
2529 chr1 110006 . A G 288.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.955;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=3.5657;MLEAC=1;MLEAF=0.500;MQ=41.04;MQ0=0;MQRankSum=-3.990;QD=5.89;ReadPosRankSum=0.251;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:317,0,813
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|
|
2530 chr1 110065 . T G 10.2 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=29;Dels=0.00;FS=5.711;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.27;MQ0=0;MQRankSum=-2.399;QD=0.35;ReadPosRankSum=-1.898;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,3:29:38:38,0,838
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|
|
2531 chr1 110066 . T G 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.038;DP=29;Dels=0.00;FS=5.711;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.27;MQ0=0;MQRankSum=-2.399;QD=0.38;ReadPosRankSum=-1.826;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,3:29:39:39,0,891
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|
2532 chr1 110176 . A G 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.745;DP=39;Dels=0.00;FS=2.780;HaplotypeScore=3.5109;MLEAC=1;MLEAF=0.500;MQ=46.75;MQ0=0;MQRankSum=-0.407;QD=13.61;ReadPosRankSum=-0.014;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T411|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_109059_110454),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:559,0,657
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|
|
2533 chr1 110245 . A G 456.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.065;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.81;MQ0=0;MQRankSum=-0.531;QD=10.88;ReadPosRankSum=-0.142;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y388|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_109059_110454),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:485,0,885
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|
|
2534 chr1 110253 . A C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.134;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.29;MQ0=0;MQRankSum=-0.744;QD=10.27;ReadPosRankSum=0.281;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S386A|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_109059_110454),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,16:44:99:480,0,992
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|
|
2535 chr1 110499 . C A 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.668;DP=57;Dels=0.00;FS=7.487;HaplotypeScore=1.9858;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=0.040;QD=15.54;ReadPosRankSum=1.365;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:914,0,969
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|
|
2536 chr1 110535 . G A 2517.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.58;MQ0=0;QD=29.61;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,65:65:99:2546,193,0
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|
|
2537 chr1 110567 . C A 1123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.335;DP=65;Dels=0.00;FS=12.462;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.072;QD=17.29;ReadPosRankSum=-0.965;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,34:65:99:1152,0,1057
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|
|
2538 chr1 110655 . A G 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.758;DP=49;Dels=0.00;FS=10.545;HaplotypeScore=1.7803;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.344;QD=18.79;ReadPosRankSum=-0.414;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,28:49:99:949,0,664
|
|
|
2539 chr1 110660 . G C 1835.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.79;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1864,141,0
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|
|
2540 chr1 110836 . G C 550.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.562;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=18.3458;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.256;QD=13.11;ReadPosRankSum=0.128;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:579,0,858
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|
|
2541 chr1 110841 . C T 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.455;DP=42;Dels=0.00;FS=1.210;HaplotypeScore=18.3458;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.025;QD=14.76;ReadPosRankSum=-0.783;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,19:42:99:648,0,793
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|
|
2542 chr1 110897 . G T 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.379;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.66;MQ0=0;MQRankSum=-0.138;QD=16.14;ReadPosRankSum=-0.344;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:577,0,566
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|
|
2543 chr1 110902 . G A 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.982;DP=36;Dels=0.00;FS=1.235;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=0.792;QD=15.33;ReadPosRankSum=-0.032;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,17:36:99:580,0,630
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|
|
2544 chr1 110931 . T A 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.913;DP=46;Dels=0.00;FS=4.246;HaplotypeScore=2.7878;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=1.242;QD=17.30;ReadPosRankSum=-1.440;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,24:46:99:824,0,677
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|
|
2545 chr1 110948 . T A 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.588;DP=55;Dels=0.00;FS=1.028;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=57.81;MQ0=0;MQRankSum=0.416;QD=17.70;ReadPosRankSum=-0.772;EFF=SYNONYMOUS_CODING(LOW|SILENT|atA/atT|I314|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,31:55:99:1002,0,664
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|
|
2546 chr1 110974 . T G 1390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.418;DP=77;Dels=0.00;FS=4.904;HaplotypeScore=1.9464;MLEAC=1;MLEAF=0.500;MQ=54.88;MQ0=3;MQRankSum=-1.165;QD=18.06;ReadPosRankSum=-0.195;EFF=SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R306|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,49:77:99:1419,0,866
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|
|
2547 chr1 111002 . G A 3102.77 . AC=2;AF=1.00;AN=2;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=0.9987;MLEAC=2;MLEAF=1.00;MQ=52.54;MQ0=3;QD=33.73;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G296|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,92:92:99:3131,241,0
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|
|
2548 chr1 111012 . A G 148.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.621;DP=99;Dels=0.00;FS=4.879;HaplotypeScore=1.9775;MLEAC=1;MLEAF=0.500;MQ=52.31;MQ0=2;MQRankSum=-2.017;QD=1.50;ReadPosRankSum=1.985;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I293T|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:85,14:99:99:177,0,2833
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|
|
2549 chr1 111037 . C T 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.209;DP=91;Dels=0.00;FS=27.980;HaplotypeScore=5.8656;MLEAC=1;MLEAF=0.500;MQ=52.14;MQ0=1;MQRankSum=-5.776;QD=7.67;ReadPosRankSum=1.097;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G285R|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:61,30:91:99:726,0,2033
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|
|
2550 chr1 111047 . C T 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.018;DP=95;Dels=0.00;FS=36.143;HaplotypeScore=18.9090;MLEAC=1;MLEAF=0.500;MQ=50.94;MQ0=2;MQRankSum=-6.952;QD=8.96;ReadPosRankSum=-0.167;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L281|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:55,39:95:99:879,0,1831
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|
|
2551 chr1 111053 . G A 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.068;DP=94;Dels=0.00;FS=22.160;HaplotypeScore=52.4073;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=2;MQRankSum=2.884;QD=5.07;ReadPosRankSum=-0.550;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y279|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:75,19:94:99:505,0,2239
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|
|
2552 chr1 111063 . G A 314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.458;DP=88;Dels=0.00;FS=26.842;HaplotypeScore=20.7019;MLEAC=1;MLEAF=0.500;MQ=49.44;MQ0=2;MQRankSum=-5.090;QD=3.58;ReadPosRankSum=-0.104;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T276M|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:67,21:88:99:343,0,2305
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|
|
2553 chr1 111093 . T G 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.555;DP=72;Dels=0.00;FS=18.592;HaplotypeScore=4.3003;MLEAC=1;MLEAF=0.500;MQ=48.32;MQ0=2;MQRankSum=-5.719;QD=9.66;ReadPosRankSum=1.059;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:40,31:72:99:724,0,1232
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|
|
2554 chr1 111097 . C T 703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.318;DP=72;Dels=0.00;FS=35.215;HaplotypeScore=4.3003;MLEAC=1;MLEAF=0.500;MQ=48.27;MQ0=2;MQRankSum=-6.753;QD=9.77;ReadPosRankSum=1.271;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,35:72:99:732,0,1245
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|
|
2555 chr1 111100 . A G 689.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.870;DP=71;Dels=0.00;FS=28.661;HaplotypeScore=4.3003;MLEAC=1;MLEAF=0.500;MQ=48.11;MQ0=2;MQRankSum=-5.937;QD=9.72;ReadPosRankSum=0.950;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:40,31:71:99:718,0,1230
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|
|
2556 chr1 111136 . T C 1449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.884;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=59.2005;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=0;MQRankSum=-5.507;QD=20.14;ReadPosRankSum=1.606;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,49:72:99:1478,0,710
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|
|
2557 chr1 111137 . T A 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.429;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=58.2007;MLEAC=1;MLEAF=0.500;MQ=51.13;MQ0=0;MQRankSum=5.353;QD=9.45;ReadPosRankSum=-1.274;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:49,22:71:99:699,0,1451
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|
|
2558 chr1 111146 . G A 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.640;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=19.0679;MLEAC=1;MLEAF=0.500;MQ=51.24;MQ0=1;MQRankSum=-5.478;QD=4.65;ReadPosRankSum=0.664;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:53,21:74:99:372,0,1862
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|
|
2559 chr1 111162 . G A 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.513;DP=77;Dels=0.00;FS=4.192;HaplotypeScore=2.5773;MLEAC=1;MLEAF=0.500;MQ=50.69;MQ0=1;MQRankSum=-4.854;QD=3.78;ReadPosRankSum=-0.383;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:57,20:77:99:319,0,1968
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|
|
2560 chr1 111178 . A G 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.787;DP=88;Dels=0.00;FS=4.774;HaplotypeScore=23.6084;MLEAC=1;MLEAF=0.500;MQ=51.68;MQ0=1;MQRankSum=-2.409;QD=9.66;ReadPosRankSum=0.590;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:58,30:88:99:878,0,1739
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|
|
2561 chr1 111187 . C T 395.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.713;DP=91;Dels=0.00;FS=21.798;HaplotypeScore=61.2603;MLEAC=1;MLEAF=0.500;MQ=52.52;MQ0=1;MQRankSum=-5.366;QD=4.35;ReadPosRankSum=-0.991;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),SPLICE_SITE_DONOR(HIGH||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:69,22:91:99:424,0,2409
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|
|
2562 chr1 111193 . A T 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.314;DP=87;Dels=0.00;FS=25.534;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.35;MQ0=1;MQRankSum=-4.830;QD=5.18;ReadPosRankSum=-0.680;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Agg|W268R|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:67,20:87:99:479,0,2299
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|
|
2563 chr1 111194 . G A 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.569;DP=87;Dels=0.00;FS=25.534;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.42;MQ0=1;MQRankSum=-4.830;QD=5.11;ReadPosRankSum=-0.649;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y267|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:67,20:87:99:473,0,2303
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|
|
2564 chr1 111218 . A G 1531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.345;DP=85;Dels=0.00;FS=28.288;HaplotypeScore=40.8045;MLEAC=1;MLEAF=0.500;MQ=53.15;MQ0=1;MQRankSum=-6.832;QD=18.02;ReadPosRankSum=0.372;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D259|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,50:85:99:1560,0,1149
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|
|
2565 chr1 111221 . A G 491.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.974;DP=85;Dels=0.00;FS=2.368;HaplotypeScore=41.6986;MLEAC=1;MLEAF=0.500;MQ=53.00;MQ0=1;MQRankSum=-0.591;QD=5.79;ReadPosRankSum=0.772;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G258|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:63,21:85:99:520,0,2174
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|
|
2566 chr1 111222 . C T 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.901;DP=85;Dels=0.00;FS=52.665;HaplotypeScore=41.6986;MLEAC=1;MLEAF=0.500;MQ=53.00;MQ0=1;MQRankSum=-6.297;QD=9.76;ReadPosRankSum=-0.509;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G258D|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:55,30:85:99:858,0,1882
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|
|
2567 chr1 111233 . C A 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.154;DP=83;Dels=0.00;FS=8.074;HaplotypeScore=21.7535;MLEAC=1;MLEAF=0.500;MQ=52.66;MQ0=0;MQRankSum=0.985;QD=6.33;ReadPosRankSum=-0.484;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P254|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:63,20:83:99:554,0,2166
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|
|
2568 chr1 111239 . C T 1826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=83;Dels=0.00;FS=18.536;HaplotypeScore=20.7540;MLEAC=1;MLEAF=0.500;MQ=52.71;MQ0=0;MQRankSum=-5.866;QD=22.01;ReadPosRankSum=-0.753;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V252|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,56:83:99:1855,0,817
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|
|
2569 chr1 111265 . T C 944.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.195;DP=74;Dels=0.00;FS=53.983;HaplotypeScore=13.9941;MLEAC=1;MLEAF=0.500;MQ=52.93;MQ0=0;MQRankSum=-6.988;QD=12.77;ReadPosRankSum=2.319;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,32:74:99:973,0,1429
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|
|
2570 chr1 111274 . T C 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.905;DP=65;Dels=0.00;FS=22.427;HaplotypeScore=13.9941;MLEAC=1;MLEAF=0.500;MQ=52.66;MQ0=0;MQRankSum=4.440;QD=9.60;ReadPosRankSum=-1.326;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,21:65:99:652,0,1525
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|
|
2571 chr1 111296 . T A 700.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.855;DP=60;Dels=0.00;FS=47.063;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.47;MQ0=0;MQRankSum=-6.194;QD=11.68;ReadPosRankSum=-0.038;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,24:60:99:729,0,1223
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|
2572 chr1 111307 . C T 533.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.080;DP=61;Dels=0.00;FS=45.484;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.52;MQ0=0;MQRankSum=-6.030;QD=8.75;ReadPosRankSum=-0.269;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:41,20:61:99:562,0,1377
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|
2573 chr1 111315 . A T 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.943;DP=53;Dels=0.00;FS=25.441;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.56;MQ0=0;MQRankSum=-4.672;QD=4.07;ReadPosRankSum=-2.694;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,10:53:99:244,0,1509
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|
|
2574 chr1 111318 . C T 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.601;DP=50;Dels=0.00;FS=22.968;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-4.247;QD=3.04;ReadPosRankSum=-2.686;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,8:50:99:180,0,1475
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|
|
2575 chr1 111328 . C T 2042.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.86;MQ0=0;QD=31.58;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2071,162,0
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|
|
2576 chr1 111397 . G A 2124.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.93;MQ0=1;QD=28.28;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2153,166,0
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|
|
2577 chr1 111485 . C T 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.983;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=1;MQRankSum=-1.024;QD=15.81;ReadPosRankSum=1.190;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q223|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111401_111565) GT:AD:DP:GQ:PL 0/1:23,26:49:99:803,0,742
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|
|
2578 chr1 111592 . T A 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.351;DP=60;Dels=0.00;FS=3.582;HaplotypeScore=1.6006;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.112;QD=13.36;ReadPosRankSum=-0.246;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:830,0,1146
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|
|
2579 chr1 111732 . A G 735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.751;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.37;MQ0=0;MQRankSum=-1.026;QD=14.15;ReadPosRankSum=1.868;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:764,0,902
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|
|
2580 chr1 111733 . G A 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.217;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=2.274;QD=17.17;ReadPosRankSum=-2.142;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:904,0,661
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|
|
2581 chr1 111744 . G A 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.681;DP=48;Dels=0.00;FS=2.691;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=0;MQRankSum=0.557;QD=16.14;ReadPosRankSum=-0.227;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:803,0,707
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|
|
2582 chr1 111927 . C T 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.084;DP=61;Dels=0.00;FS=8.983;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.791;QD=18.34;ReadPosRankSum=0.399;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q139|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111756_112103) GT:AD:DP:GQ:PL 0/1:27,34:61:99:1147,0,896
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|
|
2583 chr1 111933 . G A 1065.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.331;DP=59;Dels=0.00;FS=11.534;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.586;QD=18.06;ReadPosRankSum=0.936;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I137|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111756_112103) GT:AD:DP:GQ:PL 0/1:27,32:59:99:1094,0,890
|
|
|
2584 chr1 112070 . T C 1601.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.25;MQ0=0;QD=27.83;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I92V|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111756_112103) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1630,123,0
|
|
|
2585 chr1 112145 . T C 969.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.317;DP=47;Dels=0.00;FS=8.803;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=-2.922;QD=20.63;ReadPosRankSum=0.908;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:998,0,587
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|
|
2586 chr1 112157 . A T 1725.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=24.4498;MLEAC=2;MLEAF=1.00;MQ=58.54;MQ0=0;QD=24.37;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1754,129,0
|
|
|
2587 chr1 112214 . G A 579.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.778;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=57.89;MQ0=2;MQRankSum=0.106;QD=14.87;ReadPosRankSum=-2.021;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:608,0,645
|
|
|
2588 chr1 112312 . C G 1042.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.239;DP=44;Dels=0.00;FS=4.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-0.391;QD=23.70;ReadPosRankSum=-0.340;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:14,30:44:99:1071,0,416
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|
|
2589 chr1 112332 . G A 327.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.487;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.961;QD=7.80;ReadPosRankSum=-0.320;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,12:42:99:356,0,1063
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|
|
2590 chr1 112390 . A T 521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.639;DP=47;Dels=0.00;FS=2.499;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.835;QD=11.10;ReadPosRankSum=-0.271;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:550,0,929
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|
|
2591 chr1 112486 . A C 689.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.749;DP=57;Dels=0.00;FS=12.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=0;MQRankSum=0.008;QD=12.10;ReadPosRankSum=-1.976;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,23:57:99:718,0,1139
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|
2592 chr1 112608 . A G 846.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.099;DP=62;Dels=0.00;FS=0.979;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.596;QD=13.66;ReadPosRankSum=-0.185;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:35,27:62:99:875,0,1208
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|
2593 chr1 112714 . A C 1539.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.662;DP=44;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.46;MQ0=0;MQRankSum=-0.873;QD=34.99;ReadPosRankSum=0.817;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,42:44:59:1568,59,0
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|
2594 chr1 112726 . A G 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=45;Dels=0.00;FS=1.256;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=0.059;QD=10.97;ReadPosRankSum=-0.925;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,17:45:99:522,0,972
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|
2595 chr1 112738 . A G 1769.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.45;MQ0=0;QD=28.86;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1798,138,0
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|
|
2596 chr1 112792 . A G 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.691;DP=41;Dels=0.00;FS=7.053;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.535;QD=16.53;ReadPosRankSum=0.561;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L68|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:20,21:41:99:706,0,681
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2597 chr1 112909 . A C 1038.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.15;MQ0=0;QD=31.52;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Gtg|L29V|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,28:28:81:1067,81,0
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|
2598 chr1 112926 . A T 432.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.603;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=24.1961;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=-0.021;QD=14.43;ReadPosRankSum=-3.139;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V23D|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:14,16:30:99:461,0,376
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|
2599 chr1 112983 . A G 1239.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.7883;MLEAC=2;MLEAF=1.00;MQ=57.43;MQ0=0;QD=33.51;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V4A|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1268,99,0
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|
|
2600 chr1 112990 . T C 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.117;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=3.3109;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=0.352;QD=7.05;ReadPosRankSum=-0.185;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T2A|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:24,12:36:99:282,0,828
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|
2601 chr1 112999 . T C 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.231;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=2.4558;MLEAC=1;MLEAF=0.500;MQ=57.95;MQ0=0;MQRankSum=1.333;QD=22.16;ReadPosRankSum=-0.622;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:11,24:35:99:804,0,241
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|
2602 chr1 113028 . T C 261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=18.3184;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=-1.835;QD=9.35;ReadPosRankSum=0.000;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:17,11:28:99:290,0,593
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2603 chr1 113037 . G T 229.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.102;DP=26;Dels=0.04;FS=0.000;HaplotypeScore=20.2844;MLEAC=1;MLEAF=0.500;MQ=56.42;MQ0=0;MQRankSum=-2.110;QD=8.84;ReadPosRankSum=-0.220;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:14,9:25:99:258,0,479
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2604 chr1 113038 . A T 187.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.888;DP=25;Dels=0.04;FS=0.000;HaplotypeScore=19.2851;MLEAC=1;MLEAF=0.500;MQ=56.27;MQ0=0;MQRankSum=-0.827;QD=7.51;ReadPosRankSum=0.582;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:16,8:24:99:216,0,560
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|
2605 chr1 113090 . A C 20.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.412;DP=41;Dels=0.00;FS=2.417;HaplotypeScore=13.9009;MLEAC=1;MLEAF=0.500;MQ=55.93;MQ0=2;MQRankSum=0.949;QD=0.51;ReadPosRankSum=-0.532;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:37,4:41:49:49,0,1144
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2606 chr1 113092 . C T 1222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.600;DP=42;Dels=0.00;FS=2.442;HaplotypeScore=13.9009;MLEAC=1;MLEAF=0.500;MQ=56.03;MQ0=2;MQRankSum=-1.195;QD=29.11;ReadPosRankSum=0.789;EFF=START_GAINED(LOW||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:4,38:42:40:1251,0,40
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2607 chr1 113105 . T A 1562.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.66;MQ0=2;QD=30.97;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1591,117,0
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2608 chr1 113115 . G A 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.012;DP=45;Dels=0.00;FS=1.232;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=2;MQRankSum=1.145;QD=17.44;ReadPosRankSum=-0.628;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:18,27:45:99:813,0,572
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|
2609 chr1 113119 . G A 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.534;DP=45;Dels=0.00;FS=2.776;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.79;MQ0=2;MQRankSum=0.335;QD=11.11;ReadPosRankSum=0.907;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:28,17:45:99:528,0,850
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2610 chr1 113161 . C T 1227.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=2.5015;MLEAC=2;MLEAF=1.00;MQ=59.14;MQ0=0;QD=29.79;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,34:34:96:1256,96,0
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2611 chr1 113173 . T C 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.461;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=1.037;QD=10.59;ReadPosRankSum=0.148;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:18,12:30:99:346,0,540
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2612 chr1 113177 . T C 998.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=58.92;MQ0=0;QD=25.30;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1027,78,0
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2613 chr1 113178 . G A 1046.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=58.92;MQ0=0;QD=29.64;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,28:28:81:1075,81,0
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2614 chr1 113190 . C G 241.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.023;DP=29;Dels=0.00;FS=1.585;HaplotypeScore=1.7883;MLEAC=1;MLEAF=0.500;MQ=58.58;MQ0=0;MQRankSum=-0.665;QD=8.34;ReadPosRankSum=-1.996;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:19,10:29:99:270,0,614
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2615 chr1 113238 . G A 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.041;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=20.8374;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-0.586;QD=3.57;ReadPosRankSum=2.277;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:21,5:26:99:121,0,747
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2616 chr1 113268 . T G 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.540;DP=36;Dels=0.00;FS=5.290;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=0.353;QD=10.83;ReadPosRankSum=-0.257;EFF=START_GAINED(LOW||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:21,15:36:99:418,0,717
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2617 chr1 113287 . A C 1111.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.97;MQ0=0;QD=29.47;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,31:31:90:1140,90,0
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2618 chr1 113306 . A C 1268.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;QD=31.06;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1297,99,0
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2619 chr1 113324 . C A 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.099;DP=34;Dels=0.00;FS=1.524;HaplotypeScore=1.9977;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-0.248;QD=20.79;ReadPosRankSum=0.071;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:13,21:34:99:735,0,408
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2620 chr1 113358 . G A 385.89 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.203;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=-0.134;QD=29.68;ReadPosRankSum=1.470;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:1,12:13:2:412,0,2
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2621 chr1 113386 . A G 130.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.82;MQ0=0;QD=32.51;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,4:4:12:158,12,0
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2622 chr1 113396 . T C 43.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.00;MQ0=0;QD=21.87;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0
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2623 chr1 113410 . A T 156.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.82;MQ0=0;QD=31.38;EFF=START_GAINED(LOW||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,5:5:15:185,15,0
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2624 chr1 113431 . A G 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.920;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.03;MQ0=0;MQRankSum=1.920;QD=18.85;ReadPosRankSum=1.920;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:3,5:8:82:179,0,82
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2625 chr1 113440 . T A 180.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.82;MQ0=0;QD=26.86;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:209,15,0
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2626 chr1 113444 . T A 178.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.82;MQ0=0;QD=31.25;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:207,15,0
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|
2627 chr1 113446 . A C 181.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.82;MQ0=0;QD=27.48;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:210,15,0
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|
2628 chr1 113450 . A T 214.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.19;MQ0=0;QD=31.14;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:243,18,0
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|
2629 chr1 113468 . G C 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=48.78;MQ0=0;MQRankSum=-2.670;QD=1.59;ReadPosRankSum=-0.505;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,3:15:52:52,0,418
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|
|
2630 chr1 113483 . T C 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.061;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=52.57;MQ0=0;MQRankSum=-0.354;QD=1.10;ReadPosRankSum=-2.239;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,2:11:40:40,0,313
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2631 chr1 113488 . T C 240.8 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.39;MQ0=0;QD=30.10;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,8:8:21:269,21,0
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2632 chr1 113492 . T C 269.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.39;MQ0=0;QD=33.72;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:298,24,0
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2633 chr1 113500 . T C 242.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.30;MQ0=0;QD=34.69;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:271,21,0
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|
|
2634 chr1 113503 . T C 254.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.30;MQ0=0;QD=27.09;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:283,21,0
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|
|
2635 chr1 113505 . T C 237.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.30;MQ0=0;QD=33.97;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:266,21,0
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|
|
2636 chr1 113522 . T C 153.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.02;MQ0=0;QD=30.78;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:182,15,0
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|
|
2637 chr1 114239 . A C 56.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.00;MQ0=0;QD=28.37;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0
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|
|
2638 chr1 114264 . C G 551.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.91;MQ0=0;QD=32.00;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,15:15:42:580,42,0
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|
|
2639 chr1 114287 . G A 771.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.37;MQ0=0;QD=28.22;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,22:22:63:800,63,0
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|
|
2640 chr1 114304 . A G 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.688;DP=21;Dels=0.00;FS=5.898;HaplotypeScore=11.6441;MLEAC=1;MLEAF=0.500;MQ=54.71;MQ0=0;MQRankSum=-2.064;QD=10.66;ReadPosRankSum=-1.195;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,8:21:99:252,0,383
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|
|
2641 chr1 114311 . G A 481.18 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.217;DP=16;Dels=0.00;FS=7.270;HaplotypeScore=3.6636;MLEAC=2;MLEAF=1.00;MQ=53.36;MQ0=0;MQRankSum=-0.868;QD=30.07;ReadPosRankSum=1.302;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:1,15:16:10:509,10,0
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|
|
2642 chr1 114312 . G A 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.329;DP=16;Dels=0.00;FS=6.726;HaplotypeScore=3.6636;MLEAC=1;MLEAF=0.500;MQ=53.36;MQ0=0;MQRankSum=-2.223;QD=11.05;ReadPosRankSum=-1.799;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:205,0,294
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|
|
2643 chr1 114313 . G C 227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.261;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=3.6636;MLEAC=1;MLEAF=0.500;MQ=53.77;MQ0=0;MQRankSum=0.722;QD=13.40;ReadPosRankSum=2.646;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,8:17:99:256,0,295
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|
|
2644 chr1 114326 . T G 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.959;DP=21;Dels=0.00;FS=4.010;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.20;MQ0=0;MQRankSum=0.249;QD=12.27;ReadPosRankSum=0.107;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,9:21:99:286,0,380
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|
|
2645 chr1 114330 . T C 355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.239;DP=21;Dels=0.00;FS=4.010;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.20;MQ0=0;MQRankSum=-0.462;QD=16.94;ReadPosRankSum=-0.320;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,12:21:99:384,0,253
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|
|
2646 chr1 114353 . C A 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.002;DP=15;Dels=0.00;FS=2.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=-1.591;QD=11.18;ReadPosRankSum=-0.648;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,6:15:99:196,0,307
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|
|
2647 chr1 114354 . A T 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.237;DP=15;Dels=0.00;FS=2.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=1.945;QD=18.85;ReadPosRankSum=0.530;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,9:15:99:311,0,195
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|
|
2648 chr1 114356 . G T 283.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=15;Dels=0.00;FS=2.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=1.120;QD=18.92;ReadPosRankSum=0.530;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,9:15:99:312,0,191
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|
|
2649 chr1 114371 . G A 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.987;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=8.9971;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=-0.899;QD=13.75;ReadPosRankSum=0.417;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,13:29:99:427,0,524
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|
|
2650 chr1 114439 . T C 631.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.119;DP=37;Dels=0.00;FS=3.179;HaplotypeScore=1.5781;MLEAC=1;MLEAF=0.500;MQ=58.66;MQ0=0;MQRankSum=0.445;QD=17.07;ReadPosRankSum=0.230;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:660,0,452
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|
|
2651 chr1 114460 . C A 494.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.748;DP=36;Dels=0.00;FS=9.728;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=-0.398;QD=13.74;ReadPosRankSum=-1.894;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:523,0,607
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|
|
2652 chr1 114463 . T G 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.778;DP=35;Dels=0.00;FS=5.449;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-0.579;QD=14.34;ReadPosRankSum=2.434;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,19:35:99:530,0,535
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|
|
2653 chr1 114470 . T G 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.856;DP=26;Dels=0.00;FS=7.707;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=0;MQRankSum=1.004;QD=4.38;ReadPosRankSum=0.822;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,6:26:99:142,0,623
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|
2654 chr1 114472 . A C 864.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.84;MQ0=0;QD=34.59;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,25:25:69:893,69,0
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|
|
2655 chr1 114475 . A G 136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.177;DP=25;Dels=0.00;FS=7.952;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.84;MQ0=0;MQRankSum=-0.350;QD=5.47;ReadPosRankSum=1.813;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,6:25:99:165,0,582
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|
|
2656 chr1 114476 . G C 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.686;DP=25;Dels=0.00;FS=7.908;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.84;MQ0=0;MQRankSum=-0.223;QD=5.75;ReadPosRankSum=2.004;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,6:25:99:172,0,560
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|
2657 chr1 114480 . C A 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.623;DP=25;Dels=0.00;FS=7.952;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.84;MQ0=0;MQRankSum=-1.304;QD=5.71;ReadPosRankSum=2.450;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,6:25:99:171,0,583
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|
|
2658 chr1 114486 . T G 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.268;DP=31;Dels=0.00;FS=17.994;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.46;MQ0=0;MQRankSum=0.434;QD=8.86;ReadPosRankSum=0.681;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,11:31:99:303,0,607
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|
|
2659 chr1 114494 . C G 1000.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.13;MQ0=0;QD=30.60;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1029,78,0
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|
2660 chr1 114501 . G A 815.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.64;MQ0=0;QD=33.99;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,24:24:66:844,66,0
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|
|
2661 chr1 114552 . C T 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.040;DP=25;Dels=0.00;FS=11.090;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=0.245;QD=17.19;ReadPosRankSum=1.006;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,13:25:99:458,0,356
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|
2662 chr1 114576 . A T 643.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.58;MQ0=0;QD=37.73;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,18:18:51:672,51,0
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|
|
2663 chr1 114578 . T C 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.318;DP=24;Dels=0.00;FS=4.533;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.41;MQ0=0;MQRankSum=0.381;QD=7.32;ReadPosRankSum=1.778;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,7:24:99:204,0,601
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|
2664 chr1 114603 . A C 1082.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.79;MQ0=0;QD=29.78;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1111,84,0
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|
2665 chr1 114617 . G A 1458.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=28.9952;MLEAC=2;MLEAF=1.00;MQ=46.56;MQ0=0;QD=27.04;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1487,114,0
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|
|
2666 chr1 114621 . G A 1401.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.91;MQ0=0;QD=29.59;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1430,111,0
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|
|
2667 chr1 114645 . A G 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.436;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=37.7265;MLEAC=1;MLEAF=0.500;MQ=45.53;MQ0=0;MQRankSum=-1.288;QD=20.49;ReadPosRankSum=1.767;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:11,23:34:99:725,0,274
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|
2668 chr1 114719 . A G 12.77 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=4.26;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:39,3,0
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|
|
2669 chr1 114726 . A G 10.9 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=3.63;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:37,3,0
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|
|
2670 chr1 114739 . T C 14.68 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=4.89;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:41,3,0
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|
|
2671 chr1 114740 . C T 11.83 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=3.94;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:38,3,0
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|
|
2672 chr1 114744 . T C 15.65 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=5.22;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:42,3,0
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|
|
2673 chr1 114746 . A G 15.65 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=5.22;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:42,3,0
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|
|
2674 chr1 114752 . A G 13.72 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=4.57;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:40,3,0
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|
|
2675 chr1 114770 . G C 44.74 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.49;MQ0=0;QD=8.95;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:6:72,6,0
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|
|
2676 chr1 114788 . T C 46.74 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.96;MQ0=0;QD=11.69;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:4:6:74,6,0
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|
|
2677 chr1 114810 . T G 15.65 LowQual AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.41;MQ0=0;QD=7.83;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,2:2:3:42,3,0
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|
|
2678 chr1 114906 . T G 147.9 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.64;MQ0=0;QD=21.13;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:15:176,15,0
|
|
|
2679 chr1 114967 . A T 395.9 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.734;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.69;MQ0=0;MQRankSum=2.100;QD=28.28;ReadPosRankSum=0.822;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,12:14:15:424,15,0
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|
|
2680 chr1 115005 . G A 307.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.086;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=29.1197;MLEAC=2;MLEAF=1.00;MQ=34.93;MQ0=0;MQRankSum=1.678;QD=23.64;ReadPosRankSum=-1.086;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,11:13:9:335,9,0
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|
|
2681 chr1 115006 . C T 312.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.099;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=33.6508;MLEAC=2;MLEAF=1.00;MQ=34.93;MQ0=0;MQRankSum=1.678;QD=24.02;ReadPosRankSum=-1.086;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,11:13:9:340,9,0
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|
|
2682 chr1 115080 . G A 659.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.90;MQ0=0;QD=24.72;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:688,51,0
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|
|
2683 chr1 115081 . G A 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.722;DP=17;Dels=0.00;FS=1.957;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.90;MQ0=0;MQRankSum=0.433;QD=16.63;ReadPosRankSum=-0.433;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:8,9:17:99:311,0,275
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|
|
2684 chr1 115090 . T C 776.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.86;MQ0=0;QD=33.63;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:805,60,0
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|
|
2685 chr1 115098 . G T 841.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.28;MQ0=0;QD=32.76;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:870,66,0
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|
|
2686 chr1 115143 . A G 816.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=57.71;MQ0=0;QD=26.49;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:845,63,0
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|
|
2687 chr1 115156 . A G 687.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=57.36;MQ0=0;QD=31.79;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,19:19:54:716,54,0
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|
|
2688 chr1 115169 . T C 779.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.61;MQ0=0;QD=28.56;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,21:21:60:808,60,0
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|
|
2689 chr1 115181 . T G 1085.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.15;MQ0=0;QD=34.25;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1114,84,0
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|
|
2690 chr1 115198 . A G 817.1 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.246;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.96;MQ0=0;MQRankSum=-1.201;QD=34.05;ReadPosRankSum=2.246;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,22:24:11:845,11,0
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|
|
2691 chr1 115206 . C T 1077.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=58.19;MQ0=0;QD=34.94;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1106,81,0
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|
|
2692 chr1 115249 . G A 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.086;DP=53;Dels=0.00;FS=9.816;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.278;QD=13.15;ReadPosRankSum=-1.463;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:725,0,1025
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|
2693 chr1 115259 . A G 2107.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.59;MQ0=0;QD=29.15;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2136,166,0
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|
|
2694 chr1 115271 . A G 935.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.303;DP=57;Dels=0.00;FS=11.864;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=1.031;QD=16.42;ReadPosRankSum=-3.364;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,30:57:99:964,0,858
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|
|
2695 chr1 115276 . G T 881.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.719;DP=60;Dels=0.00;FS=6.930;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=0.956;QD=14.70;ReadPosRankSum=-2.838;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,28:60:99:910,0,1060
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|
2696 chr1 115303 . C T 2271.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=57.57;MQ0=0;QD=28.19;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2300,172,0
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|
|
2697 chr1 115305 . A G 820.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.643;DP=56;Dels=0.00;FS=5.501;HaplotypeScore=51.1251;MLEAC=1;MLEAF=0.500;MQ=57.53;MQ0=0;MQRankSum=3.741;QD=14.66;ReadPosRankSum=-0.379;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:849,0,1091
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|
2698 chr1 115352 . T C 875.96 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.787;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=0;MQRankSum=-1.250;QD=32.44;ReadPosRankSum=2.268;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,25:27:5:903,5,0
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|
2699 chr1 115355 . A G 885.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.694;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=0;MQRankSum=-1.157;QD=32.81;ReadPosRankSum=1.898;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,25:27:6:913,6,0
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|
|
2700 chr1 115360 . T C 783.56 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.463;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.98;MQ0=0;MQRankSum=-1.129;QD=31.34;ReadPosRankSum=1.965;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:3,22:25:7:811,0,7
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|
2701 chr1 115381 . A G 1182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.671;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.28;MQ0=1;MQRankSum=4.365;QD=21.12;ReadPosRankSum=5.503;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,35:56:99:1211,0,406
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|
2702 chr1 115385 . C T 2076.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.28;MQ0=1;QD=35.26;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2105,160,0
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|
2703 chr1 115399 . G T 669.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.993;DP=58;Dels=0.00;FS=5.640;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=1;MQRankSum=-3.684;QD=11.55;ReadPosRankSum=-2.448;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:698,0,1158
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|
2704 chr1 115400 . C T 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.919;DP=58;Dels=0.00;FS=5.893;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=1;MQRankSum=-2.871;QD=11.38;ReadPosRankSum=-2.415;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:688,0,1133
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|
2705 chr1 115414 . A G 1203.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=64;Dels=0.00;FS=3.517;HaplotypeScore=52.2248;MLEAC=1;MLEAF=0.500;MQ=55.46;MQ0=1;MQRankSum=2.511;QD=18.81;ReadPosRankSum=-0.519;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,35:64:99:1232,0,864
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|
2706 chr1 115418 . T C 1129.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.624;DP=66;Dels=0.00;FS=0.952;HaplotypeScore=30.9607;MLEAC=1;MLEAF=0.500;MQ=55.61;MQ0=1;MQRankSum=3.185;QD=17.12;ReadPosRankSum=0.112;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,34:66:99:1158,0,983
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2707 chr1 115440 . A C 941.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.049;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9932;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=1;MQRankSum=0.387;QD=14.95;ReadPosRankSum=2.190;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:970,0,1095
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2708 chr1 115476 . T C 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.547;DP=52;Dels=0.00;FS=1.083;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.880;QD=13.59;ReadPosRankSum=1.676;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,22:52:99:735,0,938
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2709 chr1 115480 . C A 1943.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=58.95;MQ0=0;QD=27.17;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:1972,150,0
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2710 chr1 115485 . T C 955.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=58;Dels=0.00;FS=5.136;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=0.179;QD=16.48;ReadPosRankSum=0.288;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:984,0,900
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|
2711 chr1 115540 . T C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.408;DP=54;Dels=0.00;FS=4.135;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.46;MQ0=0;MQRankSum=-0.444;QD=11.44;ReadPosRankSum=-1.047;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,21:54:99:646,0,1164
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2712 chr1 115548 . T C 2024.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.29;MQ0=0;QD=26.84;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2053,157,0
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2713 chr1 115568 . T A 987.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.17;MQ0=0;QD=26.97;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,25:25:75:1016,75,0
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2714 chr1 115569 . G A 945.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.17;MQ0=0;QD=25.19;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:974,72,0
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2715 chr1 115571 . T A 938.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.17;MQ0=0;QD=27.94;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,25:25:75:967,75,0
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2716 chr1 115574 . C T 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.756;DP=37;Dels=0.00;FS=4.170;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=0;MQRankSum=-1.454;QD=3.64;ReadPosRankSum=1.183;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,7:37:99:163,0,1074
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2717 chr1 115602 . G C 1954.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.30;MQ0=0;QD=29.47;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1983,147,0
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2718 chr1 115617 . C T 2393.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=58.36;MQ0=0;QD=29.55;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2422,184,0
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2719 chr1 115730 . A G 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.644;DP=35;Dels=0.00;FS=8.346;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.007;QD=16.96;ReadPosRankSum=-1.007;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:622,0,576
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2720 chr1 115732 . G A 512.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.309;DP=34;Dels=0.00;FS=5.871;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.103;QD=15.08;ReadPosRankSum=-1.033;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:541,0,583
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2721 chr1 115738 . G A 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.838;DP=37;Dels=0.00;FS=5.540;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=0;MQRankSum=-0.229;QD=16.99;ReadPosRankSum=-2.088;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:657,0,575
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2722 chr1 115746 . A C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.613;DP=38;Dels=0.00;FS=7.279;HaplotypeScore=2.4530;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=-0.905;QD=15.23;ReadPosRankSum=-1.401;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:607,0,655
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2723 chr1 115752 . C A 1480.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=2.4530;MLEAC=2;MLEAF=1.00;MQ=58.79;MQ0=0;QD=34.30;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1509,114,0
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2724 chr1 115793 . G A 2310.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=58.47;MQ0=0;QD=27.91;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2339,175,0
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2725 chr1 115811 . T G 668.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.352;DP=53;Dels=0.00;FS=10.487;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-2.283;QD=12.62;ReadPosRankSum=2.897;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:697,0,1114
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|
2726 chr1 115814 . T G 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.442;DP=53;Dels=0.00;FS=10.487;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-2.500;QD=12.67;ReadPosRankSum=2.987;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:700,0,1111
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|
2727 chr1 115817 . A C 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.839;DP=53;Dels=0.00;FS=8.267;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-1.670;QD=12.35;ReadPosRankSum=3.005;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:683,0,1076
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|
2728 chr1 115818 . G A 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.244;DP=53;Dels=0.00;FS=8.267;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-1.507;QD=12.73;ReadPosRankSum=2.771;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:703,0,1078
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|
2729 chr1 115819 . T A 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.977;DP=53;Dels=0.00;FS=8.267;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-1.995;QD=12.52;ReadPosRankSum=2.283;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:692,0,1062
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|
2730 chr1 115824 . T C 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.432;DP=64;Dels=0.00;FS=0.970;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=0;MQRankSum=3.857;QD=14.17;ReadPosRankSum=1.430;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:35,29:64:99:935,0,1177
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|
|
2731 chr1 115872 . T C 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.594;DP=37;Dels=0.00;FS=13.443;HaplotypeScore=16.4306;MLEAC=1;MLEAF=0.500;MQ=56.26;MQ0=0;MQRankSum=-0.564;QD=17.59;ReadPosRankSum=2.362;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:679,0,570
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|
|
2732 chr1 115884 . G T 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.378;DP=32;Dels=0.00;FS=10.606;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=56.32;MQ0=0;MQRankSum=1.397;QD=13.49;ReadPosRankSum=-2.190;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,15:32:99:460,0,582
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|
|
2733 chr1 115887 . A T 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.104;DP=30;Dels=0.00;FS=8.202;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=56.17;MQ0=0;MQRankSum=0.395;QD=16.23;ReadPosRankSum=2.058;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:14,16:30:99:515,0,435
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|
2734 chr1 115890 . T C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.658;DP=29;Dels=0.00;FS=5.988;HaplotypeScore=5.4965;MLEAC=1;MLEAF=0.500;MQ=56.14;MQ0=0;MQRankSum=-1.060;QD=15.58;ReadPosRankSum=2.211;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,15:29:99:480,0,414
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|
2735 chr1 115900 . C A 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.934;DP=29;Dels=0.00;FS=2.129;HaplotypeScore=9.4946;MLEAC=1;MLEAF=0.500;MQ=56.43;MQ0=0;MQRankSum=0.375;QD=1.51;ReadPosRankSum=-2.050;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,5:29:72:72,0,793
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|
|
2736 chr1 115966 . T A 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=49;Dels=0.00;FS=6.121;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=2;MQRankSum=0.798;QD=14.42;ReadPosRankSum=-0.543;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:735,0,712
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|
2737 chr1 115983 . T C 940.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.798;DP=55;Dels=0.00;FS=2.393;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=-0.139;QD=17.10;ReadPosRankSum=-0.278;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:969,0,769
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|
2738 chr1 115998 . C G 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.525;DP=62;Dels=0.00;FS=5.215;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=1;MQRankSum=0.776;QD=15.22;ReadPosRankSum=-0.747;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,31:62:99:972,0,1040
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|
2739 chr1 116012 . A T 917.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.443;DP=65;Dels=0.00;FS=1.013;HaplotypeScore=4.5213;MLEAC=1;MLEAF=0.500;MQ=58.32;MQ0=1;MQRankSum=0.189;QD=14.12;ReadPosRankSum=0.486;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:36,29:65:99:946,0,1099
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|
2740 chr1 116022 . G C 2223.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=2.7333;MLEAC=2;MLEAF=1.00;MQ=57.61;MQ0=1;QD=34.75;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,62:64:99:2252,175,0
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|
|
2741 chr1 116026 . T A 1054.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.724;DP=65;Dels=0.00;FS=2.157;HaplotypeScore=2.6644;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=1;MQRankSum=-0.182;QD=16.23;ReadPosRankSum=-0.155;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,35:65:99:1083,0,932
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|
|
2742 chr1 116035 . G T 2393.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=3.3036;MLEAC=2;MLEAF=1.00;MQ=57.52;MQ0=1;QD=30.09;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,65:65:99:2422,181,0
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|
2743 chr1 116068 . A G 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.699;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.75;MQ0=0;MQRankSum=-1.678;QD=17.75;ReadPosRankSum=-0.070;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:898,0,730
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|
2744 chr1 116073 . T C 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.379;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.9994;MLEAC=1;MLEAF=0.500;MQ=57.91;MQ0=0;MQRankSum=-1.194;QD=15.54;ReadPosRankSum=0.884;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,26:50:99:805,0,790
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|
2745 chr1 116082 . G A 1794.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=40.8500;MLEAC=2;MLEAF=1.00;MQ=57.87;MQ0=0;QD=31.31;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1823,138,0
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|
2746 chr1 116106 . C T 1595.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=54.1245;MLEAC=2;MLEAF=1.00;MQ=57.28;MQ0=0;QD=30.04;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1624,120,0
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|
2747 chr1 116191 . G A 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.858;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=3.7255;MLEAC=1;MLEAF=0.500;MQ=57.68;MQ0=0;MQRankSum=0.684;QD=10.49;ReadPosRankSum=-2.599;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,17:40:99:448,0,731
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|
2748 chr1 116284 . G T 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.326;DP=43;Dels=0.00;FS=1.216;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.07;MQ0=2;MQRankSum=-1.787;QD=15.72;ReadPosRankSum=-0.352;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:704,0,696
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|
2749 chr1 116327 . C T 164.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.305;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=46.31;MQ0=1;MQRankSum=-3.916;QD=5.32;ReadPosRankSum=0.305;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,8:31:99:193,0,788
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|
2750 chr1 116350 . T G 775.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.53;MQ0=0;QD=33.60;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:804,60,0
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|
2751 chr1 116354 . A G 750.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.28;MQ0=0;QD=33.75;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:779,57,0
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|
2752 chr1 116368 . G T 687.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.262;DP=24;Dels=0.00;FS=2.291;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.36;MQ0=0;MQRankSum=2.706;QD=28.66;ReadPosRankSum=1.920;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:3,21:24:26:716,0,26
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|
2753 chr1 116375 . G A 873.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.89;MQ0=0;QD=33.23;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:902,69,0
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2754 chr1 116391 . T A 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.605;DP=29;Dels=0.00;FS=7.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.81;MQ0=0;MQRankSum=-2.880;QD=4.61;ReadPosRankSum=-0.433;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,7:29:99:162,0,816
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|
2755 chr1 116393 . A T 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.688;DP=29;Dels=0.00;FS=7.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.81;MQ0=0;MQRankSum=-3.134;QD=4.65;ReadPosRankSum=-0.127;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,7:29:99:163,0,804
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|
2756 chr1 116410 . T C 1319.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.59;MQ0=0;QD=30.57;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1348,102,0
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|
2757 chr1 116422 . A G 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.301;DP=31;Dels=0.00;FS=12.035;HaplotypeScore=18.3970;MLEAC=1;MLEAF=0.500;MQ=51.97;MQ0=0;MQRankSum=-3.613;QD=9.83;ReadPosRankSum=1.590;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,11:31:99:333,0,662
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|
2758 chr1 116436 . T G 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.291;DP=37;Dels=0.00;FS=10.037;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.32;MQ0=0;MQRankSum=-1.109;QD=14.97;ReadPosRankSum=-0.957;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:582,0,665
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|
2759 chr1 116453 . C T 1640.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.49;MQ0=0;QD=26.27;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1669,123,0
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|
2760 chr1 116488 . G A 1609.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9332;MLEAC=2;MLEAF=1.00;MQ=58.82;MQ0=0;QD=32.29;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1638,123,0
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|
2761 chr1 116492 . T C 1557.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.9332;MLEAC=2;MLEAF=1.00;MQ=58.87;MQ0=0;QD=31.39;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,39:40:99:1586,117,0
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|
2762 chr1 116493 . C T 555.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.591;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9332;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=0.670;QD=13.56;ReadPosRankSum=-2.010;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:584,0,810
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|
2763 chr1 116506 . A G 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.083;DP=41;Dels=0.00;FS=2.694;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=0;MQRankSum=-2.600;QD=16.68;ReadPosRankSum=-2.058;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,21:41:99:712,0,659
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|
2764 chr1 116529 . G A 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=43;Dels=0.00;FS=2.649;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=-3.948;QD=16.90;ReadPosRankSum=2.053;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:755,0,724
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|
2765 chr1 116532 . C T 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.522;DP=43;Dels=0.00;FS=2.649;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=3.827;QD=15.97;ReadPosRankSum=-2.199;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:715,0,752
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|
2766 chr1 116537 . C T 1663.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=57.13;MQ0=0;QD=26.41;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1692,126,0
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|
2767 chr1 116554 . A C 824.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.179;DP=42;Dels=0.00;FS=9.199;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=56.68;MQ0=0;MQRankSum=-3.792;QD=19.64;ReadPosRankSum=0.436;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:853,0,555
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|
2768 chr1 116565 . C T 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.895;DP=41;Dels=0.00;FS=6.909;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=-3.782;QD=20.31;ReadPosRankSum=-0.628;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,25:41:99:861,0,489
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|
2769 chr1 116576 . G A 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=44;Dels=0.02;FS=4.546;HaplotypeScore=1.9662;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=-3.188;QD=18.47;ReadPosRankSum=-0.283;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:841,0,592
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|
2770 chr1 116582 . A T 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.054;DP=48;Dels=0.00;FS=2.552;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=56.93;MQ0=0;MQRankSum=-2.973;QD=19.66;ReadPosRankSum=-0.611;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,29:48:99:972,0,614
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|
|
2771 chr1 116595 . T G 1623.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=57.42;MQ0=0;QD=28.53;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1652,129,0
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|
|
2772 chr1 116602 . A C 1697.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.9914;MLEAC=2;MLEAF=1.00;MQ=57.59;MQ0=0;QD=31.72;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1726,138,0
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|
|
2773 chr1 116621 . G A 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.163;DP=41;Dels=0.00;FS=2.820;HaplotypeScore=1.9914;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=1.938;QD=12.04;ReadPosRankSum=-1.029;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:522,0,880
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|
2774 chr1 116650 . A G 1523.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.47;MQ0=1;QD=28.33;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1552,117,0
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|
|
2775 chr1 116679 . C T 1348.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.24;MQ0=1;QD=35.33;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1377,105,0
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|
|
2776 chr1 116681 . A G 1459.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.89;MQ0=1;QD=30.38;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1488,114,0
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|
|
2777 chr1 116708 . T C 152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.525;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.97;MQ0=0;MQRankSum=-0.735;QD=6.64;ReadPosRankSum=0.035;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,6:23:99:181,0,612
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|
|
2778 chr1 116711 . T C 651.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=20.1188;MLEAC=2;MLEAF=1.00;MQ=53.31;MQ0=0;QD=30.82;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,18:18:51:680,51,0
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|
|
2779 chr1 116712 . G A 681.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=20.1188;MLEAC=2;MLEAF=1.00;MQ=53.31;MQ0=0;QD=29.36;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:710,54,0
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|
|
2780 chr1 116724 . T A 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.705;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-0.054;QD=21.55;ReadPosRankSum=-2.007;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,10:16:99:373,0,200
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|
|
2781 chr1 116728 . T A 622.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.41;MQ0=0;QD=28.11;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:651,48,0
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|
|
2782 chr1 116732 . A G 647.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.89;MQ0=0;QD=27.29;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:676,51,0
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|
|
2783 chr1 116749 . A T 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.320;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.87;MQ0=0;MQRankSum=-0.553;QD=15.18;ReadPosRankSum=0.456;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:787,0,824
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|
|
2784 chr1 116757 . G A 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.651;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=0;MQRankSum=0.743;QD=12.68;ReadPosRankSum=1.259;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:637,0,796
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|
|
2785 chr1 116793 . G C 1565.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.26;MQ0=0;QD=26.79;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1594,120,0
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|
|
2786 chr1 116804 . T C 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.442;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=0.704;QD=12.06;ReadPosRankSum=0.418;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:559,0,846
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|
|
2787 chr1 116809 . G A 1767.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;QD=35.74;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1796,138,0
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|
|
2788 chr1 116816 . A T 1677.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.31;MQ0=0;QD=29.28;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1706,129,0
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|
|
2789 chr1 116822 . T A 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.282;DP=39;Dels=0.00;FS=1.310;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-0.493;QD=13.92;ReadPosRankSum=1.507;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:571,0,715
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|
|
2790 chr1 116824 . T C 1298.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.14;MQ0=0;QD=28.30;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1327,99,0
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|
|
2791 chr1 116906 . C A 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.057;DP=45;Dels=0.00;FS=1.192;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.149;QD=12.02;ReadPosRankSum=-2.562;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,19:45:99:569,0,916
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|
|
2792 chr1 116917 . A G 605.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.610;DP=47;Dels=0.00;FS=1.154;HaplotypeScore=1.9931;MLEAC=1;MLEAF=0.500;MQ=59.22;MQ0=0;MQRankSum=-0.501;QD=12.89;ReadPosRankSum=-2.505;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:634,0,880
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|
|
2793 chr1 116943 . A G 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.102;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.83;MQ0=0;MQRankSum=-0.695;QD=18.14;ReadPosRankSum=-2.536;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:881,0,663
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|
|
2794 chr1 116949 . G A 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.256;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=0.854;QD=13.97;ReadPosRankSum=3.146;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:713,0,926
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|
|
2795 chr1 116959 . G A 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.008;DP=55;Dels=0.00;FS=1.029;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=1.355;QD=14.94;ReadPosRankSum=2.113;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:850,0,924
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|
|
2796 chr1 116971 . G A 894.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.651;DP=50;Dels=0.00;FS=2.386;HaplotypeScore=3.2789;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=-0.283;QD=17.90;ReadPosRankSum=0.870;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:923,0,717
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|
2797 chr1 117007 . C T 1395.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.49;MQ0=0;QD=29.86;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1424,114,0
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|
|
2798 chr1 117050 . G A 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.528;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=0.324;QD=6.57;ReadPosRankSum=-1.528;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:14,5:19:99:153,0,501
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|
|
2799 chr1 117051 . A G 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.267;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.099;QD=7.10;ReadPosRankSum=-1.971;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,5:18:99:156,0,470
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|
|
2800 chr1 117054 . T G 130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.971;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.887;QD=7.26;ReadPosRankSum=-1.183;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,5:18:99:159,0,429
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|
|
2801 chr1 117071 . G A 293.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.080;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=-1.164;QD=9.79;ReadPosRankSum=0.783;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:322,0,621
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|
2802 chr1 117077 . G C 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=33;Dels=0.00;FS=1.434;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=1.029;QD=10.75;ReadPosRankSum=1.740;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:383,0,738
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|
|
2803 chr1 117104 . C T 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.641;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-2.211;QD=13.17;ReadPosRankSum=-0.335;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,21:51:99:700,0,1034
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|
2804 chr1 117130 . C A 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.251;DP=72;Dels=0.00;FS=18.205;HaplotypeScore=5.9991;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=4;MQRankSum=-4.097;QD=0.80;ReadPosRankSum=-0.505;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:61,11:72:86:86,0,2246
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|
2805 chr1 117148 . G T 1083.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.492;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=8.7758;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=1;MQRankSum=0.824;QD=14.65;ReadPosRankSum=1.709;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:39,35:74:99:1112,0,1310
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2806 chr1 117150 . C T 1112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.255;DP=75;Dels=0.00;FS=0.883;HaplotypeScore=8.7758;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=1;MQRankSum=0.114;QD=14.84;ReadPosRankSum=1.763;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:40,35:75:99:1141,0,1350
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2807 chr1 117157 . A G 1202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.476;DP=75;Dels=0.00;FS=1.938;HaplotypeScore=5.7880;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=1;MQRankSum=0.827;QD=16.04;ReadPosRankSum=2.028;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:38,37:75:99:1231,0,1283
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2808 chr1 117161 . G A 1326.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.326;DP=76;Dels=0.00;FS=3.158;HaplotypeScore=3.9994;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-1.545;QD=17.46;ReadPosRankSum=0.900;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:36,40:76:99:1355,0,1228
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2809 chr1 117175 . T G 248.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.270;DP=78;Dels=0.00;FS=22.021;HaplotypeScore=9.9969;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.164;QD=3.19;ReadPosRankSum=-2.376;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:58,12:78:99:277,0,2135
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2810 chr1 117193 . G A 892.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.099;DP=65;Dels=0.00;FS=7.705;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.404;QD=13.73;ReadPosRankSum=-0.470;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:37,28:65:99:921,0,1261
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2811 chr1 117202 . G T 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=61;Dels=0.00;FS=10.025;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=1.292;QD=12.16;ReadPosRankSum=0.170;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:37,24:61:99:770,0,1299
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2812 chr1 117240 . G A 248.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.71;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:277,21,0
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2813 chr1 117248 . A G 170.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.18;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:199,15,0
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2814 chr1 117260 . C G 86.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.76;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:114,9,0
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2815 chr1 117286 . A G 714.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.70;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:743,57,0
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2816 chr1 117350 . A T 879.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.016;DP=63;Dels=0.00;FS=4.058;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-6.819;QD=13.96;ReadPosRankSum=-3.447;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,30:63:99:908,0,1176
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2817 chr1 117353 . G A 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.169;DP=62;Dels=0.00;FS=6.115;HaplotypeScore=4.6334;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=6.744;QD=18.04;ReadPosRankSum=2.271;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,33:62:99:1147,0,898
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|
2818 chr1 117361 . T C 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.041;DP=50;Dels=0.00;FS=2.729;HaplotypeScore=10.5317;MLEAC=1;MLEAF=0.500;MQ=56.03;MQ0=0;MQRankSum=-5.755;QD=9.76;ReadPosRankSum=1.270;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:516,0,1175
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|
2819 chr1 117411 . T C 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.758;DP=23;Dels=0.00;FS=39.846;HaplotypeScore=10.9973;MLEAC=1;MLEAF=0.500;MQ=46.04;MQ0=1;MQRankSum=-3.989;QD=6.82;ReadPosRankSum=-2.011;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,11:23:99:185,0,421
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|
2820 chr1 117420 . A T 216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.462;DP=24;Dels=0.00;FS=41.720;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.07;MQ0=1;MQRankSum=-4.093;QD=9.03;ReadPosRankSum=-0.092;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:11,13:24:99:245,0,370
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2821 chr1 117422 . G T 216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.523;DP=24;Dels=0.00;FS=41.720;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.07;MQ0=1;MQRankSum=-4.093;QD=9.03;ReadPosRankSum=0.215;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:11,13:24:99:245,0,369
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2822 chr1 117438 . G C 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.413;DP=32;Dels=0.00;FS=52.903;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.12;MQ0=1;MQRankSum=-3.851;QD=17.24;ReadPosRankSum=-1.153;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,23:32:99:580,0,237
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2823 chr1 117455 . T A,G 486.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.25;MQ0=1;QD=24.31;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/2:0,9,11:20:99:628,311,284,317,0,287
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|
2824 chr1 117461 . G C 158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.770;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.298;QD=9.92;ReadPosRankSum=1.591;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:187,0,309
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|
|
2825 chr1 117462 . T C 158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.123;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.887;QD=9.92;ReadPosRankSum=1.827;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:187,0,285
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|
|
2826 chr1 117464 . C T 158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.652;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.652;QD=9.92;ReadPosRankSum=1.709;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:187,0,285
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|
|
2827 chr1 117465 . T A 157.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.416;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.062;QD=9.86;ReadPosRankSum=1.355;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:186,0,295
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|
|
2828 chr1 117467 . C T 230.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.550;DP=18;Dels=0.00;FS=28.543;HaplotypeScore=1.9990;MLEAC=1;MLEAF=0.500;MQ=54.57;MQ0=1;MQRankSum=-3.224;QD=12.82;ReadPosRankSum=0.241;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,9:18:99:259,0,257
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|
|
2829 chr1 117527 . C A 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.031;DP=38;Dels=0.00;FS=14.618;HaplotypeScore=0.9867;MLEAC=1;MLEAF=0.500;MQ=55.38;MQ0=2;MQRankSum=-4.256;QD=7.26;ReadPosRankSum=2.631;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,11:38:99:304,0,852
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|
|
2830 chr1 117551 . C G 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.950;DP=19;Dels=0.00;FS=5.815;HaplotypeScore=15.9941;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.750;QD=3.88;ReadPosRankSum=-1.750;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:15,4:19:99:102,0,544
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|
2831 chr1 117615 . A C 375.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.52;MQ0=0;QD=23.38;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:404,30,0
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|
|
2832 chr1 117624 . G A 445.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.60;MQ0=0;QD=29.19;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,12:12:36:474,36,0
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2833 chr1 117647 . T G 493.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.66;MQ0=0;QD=29.12;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,14:14:39:522,39,0
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|
2834 chr1 117656 . A G 537.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.66;MQ0=0;QD=29.60;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:566,42,0
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|
2835 chr1 117663 . A T 499.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.63;MQ0=0;QD=27.68;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:528,39,0
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|
|
2836 chr1 117688 . T C 420.53 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;QD=32.35;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,12:13:36:488,36,0
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|
2837 chr1 117772 . T G 238.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.62;MQ0=2;QD=23.88;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,10:10:21:267,21,0
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2838 chr1 117777 . A G 238.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.62;MQ0=2;QD=23.88;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,10:10:21:267,21,0
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|
2839 chr1 117778 . A G 238.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.62;MQ0=2;QD=23.88;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,10:10:21:267,21,0
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|
|
2840 chr1 117787 . C T 195.84 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.86;MQ0=2;QD=21.76;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,9:9:18:224,18,0
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|
|
2841 chr1 117923 . C T 159.9 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.922;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.24;MQ0=3;MQRankSum=1.495;QD=15.99;ReadPosRankSum=-1.495;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:5,5:10:15:188,15,0
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|
|
2842 chr1 117938 . T A 245.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=2;QD=24.58;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,8:10:21:274,21,0
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|
2843 chr1 117939 . T C 282.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=2;QD=28.28;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,8:10:24:311,24,0
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2844 chr1 117954 . T G 632.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.29;MQ0=2;QD=33.30;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,19:19:51:661,51,0
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|
2845 chr1 117967 . C T 371.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.351;DP=31;Dels=0.00;FS=12.308;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.54;MQ0=2;MQRankSum=-0.465;QD=11.99;ReadPosRankSum=-4.539;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,12:31:99:400,0,581
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|
2846 chr1 117972 . C G 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.218;DP=31;Dels=0.00;FS=12.308;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.54;MQ0=2;MQRankSum=-0.686;QD=12.02;ReadPosRankSum=-4.539;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,12:31:99:401,0,578
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|
2847 chr1 117996 . T C 314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.341;DP=34;Dels=0.00;FS=8.609;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.71;MQ0=2;MQRankSum=-1.468;QD=9.26;ReadPosRankSum=0.635;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,11:34:99:343,0,658
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|
2848 chr1 118063 . A G 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.798;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.05;MQ0=0;MQRankSum=3.026;QD=21.04;ReadPosRankSum=3.377;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,13:19:36:428,0,36
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|
2849 chr1 118067 . T A 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.792;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=50.20;MQ0=0;MQRankSum=3.170;QD=19.49;ReadPosRankSum=3.566;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:7,13:20:60:418,0,60
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|
2850 chr1 118068 . G A 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.426;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=50.20;MQ0=0;MQRankSum=3.170;QD=19.49;ReadPosRankSum=3.487;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:7,13:20:69:418,0,69
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|
2851 chr1 118069 . G A 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.483;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=52.31;MQ0=0;MQRankSum=-3.541;QD=1.07;ReadPosRankSum=-1.362;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,7:25:55:55,0,547
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|
2852 chr1 118098 . G A 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.224;DP=32;Dels=0.00;FS=5.979;HaplotypeScore=17.1556;MLEAC=1;MLEAF=0.500;MQ=54.87;MQ0=0;MQRankSum=3.923;QD=21.06;ReadPosRankSum=-0.468;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:10,22:32:99:702,0,186
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|
2853 chr1 118118 . A G 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.220;DP=42;Dels=0.00;FS=2.745;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=2.888;QD=19.30;ReadPosRankSum=-0.117;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,26:42:99:839,0,403
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|
2854 chr1 118122 . C A 382.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.130;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=57.03;MQ0=0;MQRankSum=-1.111;QD=9.81;ReadPosRankSum=-0.447;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,15:39:99:411,0,831
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|
2855 chr1 118131 . A G 556.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.931;DP=44;Dels=0.00;FS=2.548;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.24;MQ0=0;MQRankSum=-0.837;QD=12.65;ReadPosRankSum=-1.638;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:585,0,736
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|
2856 chr1 118140 . T A 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.296;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-3.047;QD=12.91;ReadPosRankSum=-0.299;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,20:46:99:622,0,857
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|
2857 chr1 118262 . C A 945.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.769;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.037;QD=21.49;ReadPosRankSum=2.452;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,28:44:99:974,0,497
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|
2858 chr1 118324 . A G 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.163;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=0;MQRankSum=-1.355;QD=10.63;ReadPosRankSum=-2.135;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:528,0,851
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|
2859 chr1 118347 . T A 946.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.543;DP=42;Dels=0.00;FS=5.576;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.69;MQ0=0;MQRankSum=-0.125;QD=22.54;ReadPosRankSum=0.181;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,30:42:99:975,0,281
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|
2860 chr1 118393 . C G 1571.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=4.1872;MLEAC=2;MLEAF=1.00;MQ=57.66;MQ0=0;QD=30.09;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1600,120,0
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|
2861 chr1 118394 . C G 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.473;DP=43;Dels=0.00;FS=9.242;HaplotypeScore=4.1872;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=1.960;QD=15.99;ReadPosRankSum=0.524;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:716,0,621
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|
2862 chr1 118403 . G A 1580.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=41.1140;MLEAC=2;MLEAF=1.00;MQ=57.24;MQ0=0;QD=27.67;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1609,123,0
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|
2863 chr1 118423 . C A,T 1500.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.60;MQ0=0;QD=30.62;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/2:0,26,23:49:99:1727,749,670,978,0,915
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|
2864 chr1 118436 . T A 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.005;DP=53;Dels=0.00;FS=5.783;HaplotypeScore=2.6648;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=0.756;QD=14.47;ReadPosRankSum=-1.770;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,26:53:99:795,0,854
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|
|
2865 chr1 118461 . T C 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;DP=47;Dels=0.00;FS=1.192;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=3;MQRankSum=1.167;QD=15.68;ReadPosRankSum=-1.190;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,27:47:99:765,0,667
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|
|
2866 chr1 118483 . G C 535.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.250;DP=44;Dels=0.00;FS=4.457;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=3;MQRankSum=-1.011;QD=12.18;ReadPosRankSum=0.197;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,21:44:99:564,0,783
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|
|
2867 chr1 118552 . C T 844.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.12;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,23:23:66:873,66,0
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|
|
2868 chr1 118569 . G A 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.242;DP=29;Dels=0.00;FS=5.142;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.85;MQ0=0;MQRankSum=-3.742;QD=0.68;ReadPosRankSum=-3.419;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,6:29:48:48,0,779
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|
|
2869 chr1 118577 . A G 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.588;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.12;MQ0=0;MQRankSum=-3.972;QD=1.53;ReadPosRankSum=-1.520;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,7:30:74:74,0,821
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|
|
2870 chr1 118586 . T C 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.704;DP=28;Dels=0.00;FS=1.906;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=-4.094;QD=3.21;ReadPosRankSum=-0.992;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,8:28:99:118,0,717
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|
|
2871 chr1 118591 . C T 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.306;DP=26;Dels=0.00;FS=4.471;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=0;MQRankSum=3.972;QD=23.84;ReadPosRankSum=0.806;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:8,18:26:99:648,0,124
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|
|
2872 chr1 118613 . C T 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.661;DP=23;Dels=0.00;FS=4.419;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=51.81;MQ0=0;MQRankSum=-3.748;QD=6.56;ReadPosRankSum=3.244;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,9:23:99:179,0,510
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|
|
2873 chr1 118618 . T A 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.346;DP=23;Dels=0.00;FS=4.419;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=51.52;MQ0=0;MQRankSum=-3.181;QD=6.60;ReadPosRankSum=3.370;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,9:23:99:180,0,492
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|
|
2874 chr1 118625 . T A 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.047;DP=18;Dels=0.00;FS=4.708;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-2.950;QD=6.32;ReadPosRankSum=2.763;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:12,6:18:99:142,0,434
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|
|
2875 chr1 118632 . G T 625.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=2.6647;MLEAC=2;MLEAF=1.00;MQ=54.35;MQ0=0;QD=34.76;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,18:18:51:654,51,0
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|
|
2876 chr1 118676 . G T 1157.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=30.42;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,31:31:90:1186,90,0
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|
|
2877 chr1 118776 . A G 1200.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=23.9732;MLEAC=2;MLEAF=1.00;MQ=59.04;MQ0=0;QD=33.35;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,35:36:99:1229,99,0
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|
|
2878 chr1 118792 . T A 957.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.04;FS=0.000;HaplotypeScore=15.9088;MLEAC=2;MLEAF=1.00;MQ=56.73;MQ0=0;QD=28.12;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,25:25:75:986,75,0
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|
|
2879 chr1 118793 . T A 946.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.04;FS=0.000;HaplotypeScore=15.9088;MLEAC=2;MLEAF=1.00;MQ=56.73;MQ0=0;QD=32.62;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,25:25:75:975,75,0
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|
|
2880 chr1 118806 . G A 1063.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.95;MQ0=0;QD=31.10;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1092,84,0
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|
|
2881 chr1 118812 . G A 1035.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.95;MQ0=0;QD=24.64;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1064,84,0
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|
|
2882 chr1 118868 . G A 529.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.576;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.61;MQ0=0;MQRankSum=-4.743;QD=17.09;ReadPosRankSum=1.211;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,17:31:99:558,0,461
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|
|
2883 chr1 118880 . C T 637.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=1.7335;MLEAC=2;MLEAF=1.00;MQ=57.15;MQ0=0;QD=33.88;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,17:17:51:666,51,0
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|
|
2884 chr1 118885 . A G 246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.530;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=1.7335;MLEAC=1;MLEAF=0.500;MQ=57.62;MQ0=0;MQRankSum=1.002;QD=15.42;ReadPosRankSum=-0.530;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,9:16:99:275,0,201
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|
|
2885 chr1 118899 . A G 656.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.35;MQ0=0;QD=30.20;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,18:18:51:685,51,0
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|
|
2886 chr1 118943 . A G 601.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.62;MQ0=6;QD=23.14;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,21:26:48:630,48,0
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|
|
2887 chr1 118947 . T A 569.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.71;MQ0=6;QD=22.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,20:25:45:598,45,0
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|
|
2888 chr1 118954 . C T 416.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.33;MQ0=6;QD=19.85;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,16:21:33:445,33,0
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|
|
2889 chr1 118958 . C T 374.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.73;MQ0=6;QD=18.74;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,15:20:30:403,30,0
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|
|
2890 chr1 118973 . C T 260.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.100;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.10;MQ0=1;MQRankSum=-0.456;QD=17.38;ReadPosRankSum=2.100;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:2,13:15:48:289,0,48
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|
|
2891 chr1 118991 . C T 229.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.347;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.50;MQ0=1;MQRankSum=1.561;QD=10.94;ReadPosRankSum=-1.734;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,20:21:33:258,33,0
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|
|
2892 chr1 119018 . C T 229.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.520;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=15.12;MQ0=5;MQRankSum=1.561;QD=9.19;ReadPosRankSum=-1.734;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,20:25:33:258,33,0
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|
2893 chr1 119028 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.598;DP=28;Dels=0.00;FS=5.880;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=24.29;MQ0=5;MQRankSum=2.693;QD=1.21;ReadPosRankSum=-2.784;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,3:28:62:62,0,217
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|
|
2894 chr1 119038 . C G 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.913;DP=27;Dels=0.00;FS=5.880;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=24.72;MQ0=5;MQRankSum=2.679;QD=2.07;ReadPosRankSum=-2.775;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,3:27:84:84,0,217
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|
2895 chr1 119044 . T A 84.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;QD=21.19;ReadPosRankSum=0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:1,3:4:27:113,0,27
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|
2896 chr1 119050 . A T 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;QD=20.94;ReadPosRankSum=0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:1,3:4:28:112,0,28
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|
2897 chr1 119051 . C G 125.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.26;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,4:4:12:153,12,0
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|
2898 chr1 119228 . A C 261.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.62;MQ0=0;QD=30.03;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,7:7:21:290,21,0
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|
2899 chr1 119229 . G A 301.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.79;MQ0=0;QD=33.85;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,8:8:24:330,24,0
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|
2900 chr1 119234 . G A 305.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.79;MQ0=0;QD=26.59;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,8:8:24:334,24,0
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|
2901 chr1 119294 . T A 812.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.23;MQ0=0;QD=26.17;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,22:22:63:841,63,0
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|
2902 chr1 119318 . T C 804.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=19.9457;MLEAC=2;MLEAF=1.00;MQ=58.88;MQ0=0;QD=34.99;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,23:23:63:833,63,0
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|
2903 chr1 119339 . A G 715.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.45;MQ0=0;QD=23.07;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,19:19:57:744,57,0
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|
2904 chr1 119555 . C A 1140.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.628;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=-1.523;QD=34.57;ReadPosRankSum=-1.628;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,32:33:96:1169,96,0
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|
2905 chr1 119677 . C T 48.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.65;MQ0=0;MQRankSum=0.736;QD=16.25;ReadPosRankSum=-0.736;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,2:3:6:76,6,0
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|
2906 chr1 119803 . C T 34.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.77;MQ0=0;QD=17.37;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,2:2:6:62,6,0
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|
2907 chr1 119816 . G A 33.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.77;MQ0=0;QD=16.87;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0
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|
2908 chr1 119819 . C T 32.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.77;MQ0=0;QD=16.37;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,2:2:6:60,6,0
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|
2909 chr1 119830 . A G 36.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.77;MQ0=0;QD=18.37;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,2:2:6:64,6,0
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|
2910 chr1 119840 . C T 68.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=0;QD=22.76;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:3:9:96,9,0
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2911 chr1 119841 . T C 65.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=0;QD=21.76;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:3:9:93,9,0
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2912 chr1 119862 . G T 73.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=0;QD=24.43;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:3:9:101,9,0
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|
2913 chr1 119869 . T C 73.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=0;QD=24.43;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:3:9:101,9,0
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|
2914 chr1 119921 . A T 289.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=61.65;MQ0=0;QD=30.13;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,8:8:24:318,24,0
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|
2915 chr1 119961 . G C 77.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=65.19;MQ0=0;MQRankSum=0.727;QD=19.44;ReadPosRankSum=0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:1,3:4:26:106,0,26
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|
2916 chr1 119977 . T G 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=13;Dels=0.00;FS=9.792;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.49;MQ0=0;MQRankSum=-1.466;QD=19.52;ReadPosRankSum=0.849;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:4,9:13:99:282,0,121
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|
2917 chr1 120103 . C G 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.398;DP=41;Dels=0.00;FS=9.770;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.26;MQ0=0;MQRankSum=0.468;QD=3.29;ReadPosRankSum=1.299;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,7:41:99:163,0,1266
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|
2918 chr1 120119 . G A 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.960;DP=37;Dels=0.00;FS=4.862;HaplotypeScore=2.9458;MLEAC=1;MLEAF=0.500;MQ=60.29;MQ0=0;MQRankSum=0.258;QD=14.67;ReadPosRankSum=-0.623;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,19:37:99:571,0,599
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|
2919 chr1 120128 . T C 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.522;DP=34;Dels=0.00;FS=3.329;HaplotypeScore=1.9459;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=1;MQRankSum=1.099;QD=15.88;ReadPosRankSum=-0.594;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,18:34:99:568,0,540
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|
2920 chr1 120143 . T C 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.282;DP=27;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=1;MQRankSum=1.487;QD=14.95;ReadPosRankSum=0.154;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,14:27:99:432,0,438
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|
2921 chr1 120179 . C T 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.897;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=1;MQRankSum=-0.517;QD=13.45;ReadPosRankSum=0.680;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,12:26:99:378,0,440
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|
2922 chr1 120186 . T C 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.610;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.83;MQ0=1;MQRankSum=-0.268;QD=12.74;ReadPosRankSum=0.903;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,12:28:99:385,0,463
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|
2923 chr1 120227 . C T 580.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.140;DP=38;Dels=0.00;FS=5.023;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=1;MQRankSum=1.322;QD=15.28;ReadPosRankSum=-1.565;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,18:38:99:609,0,620
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|
2924 chr1 120238 . T C 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.421;DP=41;Dels=0.00;FS=7.160;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=1;MQRankSum=-0.231;QD=16.41;ReadPosRankSum=0.177;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,23:41:99:701,0,597
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|
2925 chr1 120278 . C A 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=49;Dels=0.00;FS=4.269;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=1;MQRankSum=0.282;QD=18.55;ReadPosRankSum=-0.366;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,29:49:99:937,0,665
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|
|
2926 chr1 120311 . T C 694.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.855;DP=42;Dels=0.00;FS=1.163;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.780;QD=16.54;ReadPosRankSum=0.101;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,21:42:99:723,0,713
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|
|
2927 chr1 120315 . G A 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.790;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.036;QD=15.72;ReadPosRankSum=0.158;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,21:43:99:704,0,762
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|
|
2928 chr1 120371 . T C 692.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.27;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,19:19:54:721,54,0
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|
|
2929 chr1 120437 . C T 448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.001;DP=32;Dels=0.00;FS=22.212;HaplotypeScore=1.9985;MLEAC=1;MLEAF=0.500;MQ=58.32;MQ0=0;MQRankSum=-1.284;QD=14.02;ReadPosRankSum=-0.340;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,15:32:99:477,0,541
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|
|
2930 chr1 120508 . C T 1393.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=58.10;MQ0=0;QD=30.77;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1422,108,0
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|
|
2931 chr1 120513 . C G 436.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;DP=35;Dels=0.00;FS=5.287;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=0;MQRankSum=-1.317;QD=12.48;ReadPosRankSum=0.883;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,15:35:99:465,0,629
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|
|
2932 chr1 120525 . G A 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.734;DP=32;Dels=0.00;FS=5.486;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=55.77;MQ0=1;MQRankSum=0.337;QD=12.46;ReadPosRankSum=0.576;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,15:32:99:427,0,557
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|
|
2933 chr1 120532 . T A 382.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;DP=34;Dels=0.00;FS=7.806;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=55.37;MQ0=1;MQRankSum=-0.055;QD=11.26;ReadPosRankSum=0.856;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,15:34:99:411,0,622
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|
|
2934 chr1 120546 . C A 1112.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.7256;MLEAC=2;MLEAF=1.00;MQ=55.59;MQ0=1;QD=34.77;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,32:32:90:1141,90,0
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|
|
2935 chr1 120550 . C G 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.115;DP=33;Dels=0.00;FS=3.269;HaplotypeScore=2.4595;MLEAC=1;MLEAF=0.500;MQ=55.36;MQ0=1;MQRankSum=-0.422;QD=10.60;ReadPosRankSum=0.806;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,14:33:99:378,0,603
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|
|
2936 chr1 120567 . A T 60.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=25;Dels=0.00;FS=2.671;HaplotypeScore=15.7066;MLEAC=1;MLEAF=0.500;MQ=53.60;MQ0=1;MQRankSum=-2.312;QD=2.43;ReadPosRankSum=1.987;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,5:25:89:89,0,628
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|
|
2937 chr1 120592 . G C 609.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=1.9995;MLEAC=2;MLEAF=1.00;MQ=55.83;MQ0=0;QD=31.95;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,17:17:51:638,51,0
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|
|
2938 chr1 120670 . A G 746.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.31;MQ0=0;QD=33.94;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,22:22:60:775,60,0
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|
|
2939 chr1 120698 . C T 666.53 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.689;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=51.16;MQ0=0;MQRankSum=2.693;QD=28.98;ReadPosRankSum=0.959;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:3,20:23:3:693,0,3
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|
2940 chr1 120702 . G A 755.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=1.6006;MLEAC=2;MLEAF=1.00;MQ=50.14;MQ0=0;QD=34.35;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,22:22:63:784,63,0
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|
2941 chr1 120717 . T C 686.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=1.7333;MLEAC=2;MLEAF=1.00;MQ=47.61;MQ0=0;QD=34.34;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,20:20:57:715,57,0
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|
2942 chr1 120722 . T C 592.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.851;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=46.92;MQ0=0;MQRankSum=3.000;QD=28.23;ReadPosRankSum=-0.403;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:4,17:21:43:621,0,43
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|
2943 chr1 120723 . G T 738.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=46.92;MQ0=0;QD=32.21;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,21:21:60:767,60,0
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|
2944 chr1 120725 . G T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.120;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=46.92;MQ0=0;MQRankSum=-3.090;QD=0.71;ReadPosRankSum=0.224;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,4:21:43:43,0,578
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|
2945 chr1 120730 . T C 86.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.805;DP=23;Dels=0.00;FS=1.935;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.58;MQ0=0;MQRankSum=-2.065;QD=3.77;ReadPosRankSum=-0.805;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,6:23:99:115,0,600
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|
2946 chr1 120744 . C A 521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.752;DP=27;Dels=0.00;FS=1.574;HaplotypeScore=6.9985;MLEAC=1;MLEAF=0.500;MQ=46.78;MQ0=0;MQRankSum=1.604;QD=19.32;ReadPosRankSum=0.864;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,16:27:99:550,0,301
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|
2947 chr1 120759 . T C 295.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.164;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.96;MQ0=0;MQRankSum=-0.367;QD=15.57;ReadPosRankSum=-1.347;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,10:19:99:324,0,285
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|
2948 chr1 120764 . T A 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.936;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.60;MQ0=0;MQRankSum=-0.599;QD=13.70;ReadPosRankSum=0.951;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,10:21:99:316,0,375
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|
2949 chr1 120777 . C T 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.459;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=0;MQRankSum=1.257;QD=12.14;ReadPosRankSum=-0.018;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,14:33:99:429,0,613
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|
2950 chr1 120780 . G A 417.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.623;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=46.32;MQ0=0;MQRankSum=0.960;QD=11.94;ReadPosRankSum=0.354;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,14:35:99:446,0,633
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|
2951 chr1 120787 . A G 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.328;DP=39;Dels=0.00;FS=1.273;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=48.62;MQ0=0;MQRankSum=-1.898;QD=14.64;ReadPosRankSum=2.102;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,19:39:99:599,0,603
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|
2952 chr1 120802 . T C 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.444;DP=45;Dels=0.00;FS=2.555;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=50.94;MQ0=0;MQRankSum=-3.970;QD=16.39;ReadPosRankSum=1.331;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,24:45:99:766,0,656
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|
2953 chr1 120813 . A T 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.329;DP=45;Dels=0.00;FS=1.154;HaplotypeScore=13.9933;MLEAC=1;MLEAF=0.500;MQ=52.02;MQ0=0;MQRankSum=4.507;QD=14.68;ReadPosRankSum=-0.102;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,22:45:99:689,0,762
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|
2954 chr1 120816 . A G 627.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.013;DP=41;Dels=0.00;FS=2.837;HaplotypeScore=13.9933;MLEAC=1;MLEAF=0.500;MQ=51.82;MQ0=0;MQRankSum=-4.264;QD=15.31;ReadPosRankSum=0.639;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,20:41:99:656,0,729
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|
2955 chr1 120820 . T C 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.817;DP=40;Dels=0.00;FS=2.785;HaplotypeScore=13.9933;MLEAC=1;MLEAF=0.500;MQ=52.25;MQ0=0;MQRankSum=-4.361;QD=15.12;ReadPosRankSum=1.517;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,19:40:99:633,0,684
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|
2956 chr1 120826 . A G 1504.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=13.9933;MLEAC=2;MLEAF=1.00;MQ=52.41;MQ0=0;QD=34.96;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1533,114,0
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|
2957 chr1 120838 . A C 1759.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.71;MQ0=1;QD=34.54;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1788,135,0
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|
2958 chr1 120862 . T C 1676.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.45;MQ0=1;QD=31.05;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1705,132,0
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|
2959 chr1 120875 . C T 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.870;DP=43;Dels=0.00;FS=4.561;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=1;MQRankSum=-5.022;QD=11.48;ReadPosRankSum=2.076;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,18:43:99:522,0,781
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|
2960 chr1 120891 . T C 72.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.826;DP=23;Dels=0.00;FS=9.132;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.13;MQ0=0;MQRankSum=-3.019;QD=3.16;ReadPosRankSum=1.155;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,5:23:99:101,0,602
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|
2961 chr1 120906 . C A 986.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=18.7330;MLEAC=2;MLEAF=1.00;MQ=54.05;MQ0=1;QD=27.45;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1015,78,0
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|
2962 chr1 120925 . T A 452.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.177;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.81;MQ0=1;MQRankSum=-1.123;QD=12.24;ReadPosRankSum=0.578;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,16:37:99:481,0,688
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|
2963 chr1 120936 . T A 1380.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.96;MQ0=1;QD=27.06;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1409,108,0
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|
2964 chr1 120960 . G C 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.936;DP=43;Dels=0.00;FS=2.659;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=1;MQRankSum=-1.055;QD=18.34;ReadPosRankSum=-1.309;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,24:43:99:817,0,617
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|
|
2965 chr1 120966 . T C 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.430;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=1;MQRankSum=-1.213;QD=16.55;ReadPosRankSum=-0.480;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,23:43:99:740,0,631
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|
2966 chr1 120969 . G A 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.851;DP=43;Dels=0.00;FS=1.149;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=1;MQRankSum=1.322;QD=15.13;ReadPosRankSum=-0.340;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,21:43:99:679,0,731
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|
2967 chr1 120992 . C T 1474.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.45;MQ0=1;QD=25.94;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1503,111,0
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|
2968 chr1 120994 . C G 1506.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.25;MQ0=0;QD=33.17;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1535,114,0
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|
|
2969 chr1 121003 . A G 1781.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=30.81;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1810,135,0
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|
|
2970 chr1 121015 . T C 903.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.582;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=0.989;QD=17.38;ReadPosRankSum=0.659;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,27:52:99:932,0,820
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|
|
2971 chr1 121034 . T C 831.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.450;DP=49;Dels=0.00;FS=1.117;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=-0.850;QD=16.97;ReadPosRankSum=0.370;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,25:49:99:860,0,817
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|
|
2972 chr1 121052 . G A 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.516;DP=46;Dels=0.00;FS=8.862;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;MQRankSum=-0.022;QD=16.80;ReadPosRankSum=0.681;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,23:46:99:801,0,734
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|
|
2973 chr1 121087 . G T 336.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.047;DP=40;Dels=0.00;FS=5.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=0;MQRankSum=0.924;QD=8.42;ReadPosRankSum=0.579;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,16:40:99:365,0,767
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|
|
2974 chr1 121102 . G T 1242.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.72;MQ0=0;QD=33.06;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1271,99,0
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|
2975 chr1 121118 . T A 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.099;DP=22;Dels=0.00;FS=7.025;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-0.692;QD=16.94;ReadPosRankSum=0.890;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:10,12:22:99:401,0,296
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|
2976 chr1 121148 . G A 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.510;DP=27;Dels=0.00;FS=9.204;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=57.69;MQ0=0;MQRankSum=-0.655;QD=15.92;ReadPosRankSum=-0.849;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,14:27:99:458,0,425
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|
|
2977 chr1 121152 . T C 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.256;DP=26;Dels=0.00;FS=6.455;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=0;MQRankSum=-0.923;QD=15.84;ReadPosRankSum=-0.821;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,13:26:99:440,0,417
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|
|
2978 chr1 121153 . C T 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.333;DP=26;Dels=0.00;FS=6.455;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=0;MQRankSum=-0.615;QD=15.76;ReadPosRankSum=-0.872;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,13:26:99:438,0,430
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|
|
2979 chr1 121409 . T C 11.83 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.00;MQ0=0;QD=11.83;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0
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|
|
2980 chr1 121415 . G A 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.544;DP=32;Dels=0.00;FS=8.557;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.15;MQ0=0;MQRankSum=-2.657;QD=11.24;ReadPosRankSum=-0.094;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,16:32:99:388,0,539
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|
|
2981 chr1 121429 . C T 1575.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=46.16;MQ0=0;QD=22.24;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1604,126,0
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|
|
2982 chr1 121448 . T C 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.767;DP=43;Dels=0.00;FS=11.590;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.05;MQ0=0;MQRankSum=3.811;QD=14.79;ReadPosRankSum=0.158;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,20:43:99:664,0,751
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|
|
2983 chr1 121451 . G A 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.157;DP=43;Dels=0.00;FS=11.590;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.05;MQ0=0;MQRankSum=-3.859;QD=16.34;ReadPosRankSum=0.816;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,23:43:99:731,0,659
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|
|
2984 chr1 121462 . T A 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155;DP=40;Dels=0.00;FS=9.593;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.80;MQ0=0;MQRankSum=-4.391;QD=16.62;ReadPosRankSum=0.204;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,22:40:99:693,0,595
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|
|
2985 chr1 121471 . G C 11.83 LowQual AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=15.49;MQ0=14;QD=0.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:14,1:15:3:38,3,0
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|
|
2986 chr1 122095 . T C 15.65 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=15.65;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0
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|
|
2987 chr1 122148 . T G 1209.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9947;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=0;QD=35.61;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1238,93,0
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|
|
2988 chr1 122173 . G T 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.745;DP=41;Dels=0.00;FS=1.248;HaplotypeScore=3.6993;MLEAC=1;MLEAF=0.500;MQ=57.38;MQ0=0;MQRankSum=0.176;QD=15.77;ReadPosRankSum=0.311;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,20:41:99:675,0,610
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|
|
2989 chr1 122179 . T C 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.298;DP=44;Dels=0.00;FS=2.744;HaplotypeScore=2.7126;MLEAC=1;MLEAF=0.500;MQ=57.20;MQ0=0;MQRankSum=-0.813;QD=14.45;ReadPosRankSum=1.190;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,20:44:99:664,0,726
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|
|
2990 chr1 122203 . A C 703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.560;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.51;MQ0=0;MQRankSum=-2.415;QD=16.76;ReadPosRankSum=0.352;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,21:42:99:732,0,674
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|
|
2991 chr1 122216 . C G 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.587;DP=41;Dels=0.00;FS=2.755;HaplotypeScore=32.8942;MLEAC=1;MLEAF=0.500;MQ=55.52;MQ0=0;MQRankSum=-1.343;QD=15.60;ReadPosRankSum=-0.117;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,20:41:99:668,0,646
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|
|
2992 chr1 122277 . T C 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.946;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=8.4826;MLEAC=1;MLEAF=0.500;MQ=55.18;MQ0=0;MQRankSum=1.650;QD=9.49;ReadPosRankSum=2.750;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,10:30:99:313,0,658
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|
|
2993 chr1 122295 . G A 1172.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.24;MQ0=0;QD=26.60;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,31:31:90:1201,90,0
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|
|
2994 chr1 122297 . G A 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.136;DP=32;Dels=0.00;FS=3.151;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=0.564;QD=11.15;ReadPosRankSum=2.511;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,12:32:99:385,0,654
|
|
|
2995 chr1 122301 . C T 1251.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.29;MQ0=0;QD=36.50;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1280,93,0
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|
|
2996 chr1 122383 . C T 1913.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.9989;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;QD=25.00;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1942,144,0
|
|
|
2997 chr1 122415 . G A 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.015;DP=43;Dels=0.00;FS=2.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.30;MQ0=0;MQRankSum=-0.135;QD=13.41;ReadPosRankSum=-0.746;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,19:43:99:605,0,828
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|
|
2998 chr1 122424 . G A 1618.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.58;MQ0=0;QD=29.06;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1647,129,0
|
|
|
2999 chr1 122430 . G A 783.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.699;DP=43;Dels=0.00;FS=6.548;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.37;MQ0=1;MQRankSum=0.216;QD=18.23;ReadPosRankSum=-0.928;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,24:43:99:812,0,558
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|
|
3000 chr1 122455 . G A,T 921.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=45.04;MQ0=2;QD=24.90;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/2:0,20,17:37:99:1105,544,493,561,0,513
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|
|
3001 chr1 122456 . G T 462.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.745;DP=37;Dels=0.00;FS=5.023;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.04;MQ0=2;MQRankSum=-0.480;QD=12.51;ReadPosRankSum=-0.712;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,20:37:99:491,0,496
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|
|
3002 chr1 122464 . G A 961.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.23;MQ0=2;QD=30.06;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,32:32:84:990,84,0
|
|
|
3003 chr1 122469 . A G 726.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=37.29;MQ0=2;QD=27.95;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,26:26:66:755,66,0
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|
|
3004 chr1 122471 . G A 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=26;Dels=0.00;FS=3.892;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=37.29;MQ0=2;MQRankSum=1.101;QD=11.64;ReadPosRankSum=-0.811;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,12:26:99:331,0,295
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|
|
3005 chr1 122483 . G A 191.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.303;DP=23;Dels=0.00;FS=4.036;HaplotypeScore=10.7857;MLEAC=1;MLEAF=0.500;MQ=35.66;MQ0=2;MQRankSum=-2.429;QD=8.34;ReadPosRankSum=2.429;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,12:23:99:220,0,312
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|
|
3006 chr1 122487 . T A 132.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.241;DP=20;Dels=0.05;FS=1.957;HaplotypeScore=10.7857;MLEAC=1;MLEAF=0.500;MQ=31.84;MQ0=2;MQRankSum=-2.454;QD=6.64;ReadPosRankSum=2.742;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,10:19:99:161,0,242
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|
|
3007 chr1 122498 . T C 588.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.141;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=3.9968;MLEAC=1;MLEAF=0.500;MQ=48.55;MQ0=1;MQRankSum=0.407;QD=14.02;ReadPosRankSum=-0.039;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,19:42:99:617,0,646
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|
|
3008 chr1 122513 . T G 1544.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.78;MQ0=1;QD=34.33;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1573,120,0
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|
|
3009 chr1 122548 . C T 679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.027;DP=35;Dels=0.00;FS=1.445;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=0.791;QD=19.42;ReadPosRankSum=2.576;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,21:35:99:708,0,420
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|
|
3010 chr1 122565 . A T 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.454;DP=37;Dels=0.00;FS=7.957;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=0.391;QD=20.07;ReadPosRankSum=-0.673;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,23:37:99:771,0,457
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|
|
3011 chr1 122594 . G T 661.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=54;Dels=0.00;FS=2.373;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.37;MQ0=0;MQRankSum=0.177;QD=12.25;ReadPosRankSum=2.129;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,21:54:99:690,0,1043
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|
|
3012 chr1 122607 . G C 917.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=59;Dels=0.00;FS=3.662;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.387;QD=15.56;ReadPosRankSum=-0.751;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,28:59:99:946,0,1029
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|
|
3013 chr1 122655 . T G 629.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.488;DP=64;Dels=0.00;FS=1.017;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=-0.915;QD=9.84;ReadPosRankSum=1.687;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,21:64:99:658,0,1417
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|
|
3014 chr1 122658 . C G 587.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=63;Dels=0.00;FS=2.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=0;MQRankSum=0.303;QD=9.33;ReadPosRankSum=1.676;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,20:63:99:616,0,1391
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|
|
3015 chr1 122661 . C T 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.722;DP=59;Dels=0.00;FS=3.946;HaplotypeScore=7.7321;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-0.511;QD=9.88;ReadPosRankSum=1.371;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:40,19:59:99:611,0,1272
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|
|
3016 chr1 122745 . C A 1546.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=14.4976;MLEAC=2;MLEAF=1.00;MQ=56.58;MQ0=0;QD=35.56;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1575,120,0
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|
|
3017 chr1 122757 . A C,G 1142.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.27;MQ0=0;QD=30.87;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/2:0,15,22:37:99:1336,829,786,508,0,441
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|
|
3018 chr1 122760 . T G 1421.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.36;MQ0=0;QD=30.21;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1450,108,0
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|
|
3019 chr1 122767 . A C 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.798;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.03;MQ0=0;MQRankSum=-5.113;QD=8.09;ReadPosRankSum=2.844;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,13:41:99:360,0,994
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|
|
3020 chr1 122789 . C G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.173;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=-4.915;QD=8.73;ReadPosRankSum=1.209;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,12:38:99:360,0,925
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|
|
3021 chr1 122826 . G A 111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.987;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.84;MQ0=0;MQRankSum=-3.853;QD=3.02;ReadPosRankSum=1.957;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,6:37:99:140,0,1158
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|
|
3022 chr1 122828 . G A 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.592;DP=40;Dels=0.00;FS=1.550;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-2.688;QD=4.42;ReadPosRankSum=0.423;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,8:40:99:205,0,1171
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|
|
3023 chr1 122865 . C T 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.439;DP=49;Dels=0.00;FS=14.272;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=0.373;QD=9.81;ReadPosRankSum=0.501;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,16:49:99:509,0,1184
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|
|
3024 chr1 122905 . C T 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.019;DP=42;Dels=0.00;FS=5.692;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.69;MQ0=0;MQRankSum=-0.989;QD=6.14;ReadPosRankSum=0.901;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,10:42:99:286,0,1168
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|
|
3025 chr1 122938 . C T 313.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.284;DP=41;Dels=0.00;FS=5.664;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=1;MQRankSum=-4.235;QD=7.65;ReadPosRankSum=-3.497;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,13:41:99:342,0,1011
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|
|
3026 chr1 122969 . T C 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.007;DP=52;Dels=0.00;FS=11.610;HaplotypeScore=2.8266;MLEAC=1;MLEAF=0.500;MQ=58.04;MQ0=0;MQRankSum=-5.166;QD=13.00;ReadPosRankSum=1.641;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,21:52:99:704,0,1092
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|
|
3027 chr1 122976 . C T 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.424;DP=49;Dels=0.00;FS=12.245;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-3.283;QD=13.83;ReadPosRankSum=2.879;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:706,0,952
|
|
|
3028 chr1 122990 . C T 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.759;DP=52;Dels=0.00;FS=15.894;HaplotypeScore=2.9996;MLEAC=1;MLEAF=0.500;MQ=58.08;MQ0=0;MQRankSum=-4.241;QD=12.23;ReadPosRankSum=3.207;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,20:52:99:664,0,1073
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|
|
3029 chr1 123012 . C T 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.417;DP=52;Dels=0.00;FS=6.555;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=0;MQRankSum=-3.786;QD=11.46;ReadPosRankSum=0.019;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:624,0,1045
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|
|
3030 chr1 123034 . T C 470.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.523;DP=46;Dels=0.00;FS=4.428;HaplotypeScore=3.8314;MLEAC=1;MLEAF=0.500;MQ=58.65;MQ0=0;MQRankSum=-1.707;QD=10.23;ReadPosRankSum=-1.707;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:29,17:46:99:499,0,1020
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|
|
3031 chr1 123098 . A G 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.078;DP=38;Dels=0.00;FS=7.718;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=1;MQRankSum=1.769;QD=9.86;ReadPosRankSum=-1.613;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:403,0,787
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|
|
3032 chr1 123121 . C T 335.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.802;DP=35;Dels=0.00;FS=3.247;HaplotypeScore=1.8273;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=1;MQRankSum=-1.207;QD=9.59;ReadPosRankSum=-1.907;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,14:35:99:364,0,645
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|
|
3033 chr1 123176 . A T 1326.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.74;MQ0=0;QD=34.79;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1355,102,0
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|
|
3034 chr1 123262 . G A 661.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=10.6984;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.09;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:690,51,0
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|
|
3035 chr1 123294 . A G 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.444;DP=22;Dels=0.00;FS=6.897;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.901;QD=10.03;ReadPosRankSum=-0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,8:22:99:249,0,484
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|
|
3036 chr1 123320 . T A 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.094;DP=23;Dels=0.00;FS=7.060;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.409;QD=11.56;ReadPosRankSum=2.425;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,9:23:99:294,0,487
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|
|
3037 chr1 123328 . G C 229.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=25;Dels=0.00;FS=6.402;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.878;QD=9.19;ReadPosRankSum=2.123;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:258,0,573
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|
|
3038 chr1 123528 . G T 563.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.41;MQ0=3;QD=31.32;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:3,15:18:45:592,45,0
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|
|
3039 chr1 123588 . T C 848.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.28;MQ0=3;QD=33.95;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:3,22:25:66:877,66,0
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|
|
3040 chr1 123694 . A G 697.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.64;MQ0=0;QD=34.89;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,20:20:54:726,54,0
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|
|
3041 chr1 123730 . T A 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.228;DP=23;Dels=0.00;FS=5.969;HaplotypeScore=1.6281;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=0;MQRankSum=-0.502;QD=1.34;ReadPosRankSum=-0.411;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,3:23:59:59,0,664
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|
|
3042 chr1 123755 . C A 61.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=28;Dels=0.00;FS=5.305;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=0.624;QD=2.21;ReadPosRankSum=0.492;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,4:28:90:90,0,768
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|
|
3043 chr1 123843 . T C 181.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.826;DP=24;Dels=0.00;FS=16.510;HaplotypeScore=1.8663;MLEAC=1;MLEAF=0.500;MQ=58.48;MQ0=0;MQRankSum=0.889;QD=7.57;ReadPosRankSum=-0.191;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,7:24:99:210,0,577
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|
|
3044 chr1 123903 . T A 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.580;DP=31;Dels=0.00;FS=1.446;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.500;QD=11.77;ReadPosRankSum=1.221;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,13:31:99:393,0,627
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|
|
3045 chr1 123904 . G A 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.340;DP=31;Dels=0.00;FS=1.446;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.941;QD=11.67;ReadPosRankSum=1.141;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,13:31:99:390,0,619
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|
|
3046 chr1 123916 . T G 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.496;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=-1.276;QD=10.49;ReadPosRankSum=0.390;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,13:34:99:385,0,693
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|
|
3047 chr1 123923 . C T 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.989;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=0.329;QD=9.32;ReadPosRankSum=-0.141;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:373,0,791
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|
|
3048 chr1 123947 . C A 405.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.067;DP=42;Dels=0.00;FS=1.259;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=-1.321;QD=9.66;ReadPosRankSum=-0.867;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,14:42:99:434,0,970
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|
|
3049 chr1 123966 . G A 320.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.824;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=11.9954;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-0.893;QD=8.91;ReadPosRankSum=-0.275;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,11:36:99:349,0,885
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|
|
3050 chr1 123975 . T A 393.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.746;DP=41;Dels=0.00;FS=1.345;HaplotypeScore=13.9928;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.124;QD=9.60;ReadPosRankSum=1.113;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,14:41:99:422,0,967
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|
|
3051 chr1 124035 . T C 365.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.216;DP=34;Dels=0.00;FS=6.057;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=0;MQRankSum=-0.378;QD=10.76;ReadPosRankSum=1.423;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,12:34:99:394,0,689
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|
3052 chr1 124057 . G A 482.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.547;DP=38;Dels=0.00;FS=1.301;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=-0.990;QD=12.70;ReadPosRankSum=0.754;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:511,0,655
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|
|
3053 chr1 124075 . T G 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.223;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=14.4976;MLEAC=1;MLEAF=0.500;MQ=55.88;MQ0=0;MQRankSum=-0.800;QD=11.92;ReadPosRankSum=1.082;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,11:28:99:362,0,542
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|
|
3054 chr1 124090 . T C 424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.741;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.22;MQ0=0;MQRankSum=-3.362;QD=13.27;ReadPosRankSum=0.703;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,14:32:99:453,0,623
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|
|
3055 chr1 124097 . G A 315.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.142;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.10;MQ0=0;MQRankSum=-3.549;QD=10.19;ReadPosRankSum=0.669;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,12:31:99:344,0,678
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|
|
3056 chr1 124108 . A G 280.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.822;DP=29;Dels=0.00;FS=3.834;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.38;MQ0=0;MQRankSum=-4.061;QD=9.68;ReadPosRankSum=1.124;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:309,0,669
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|
|
3057 chr1 124113 . C A 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.297;DP=32;Dels=0.00;FS=6.057;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.25;MQ0=0;MQRankSum=-3.923;QD=8.52;ReadPosRankSum=1.159;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:301,0,784
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|
|
3058 chr1 124123 . A C 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.866;DP=31;Dels=0.00;FS=6.205;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-3.867;QD=8.61;ReadPosRankSum=-0.063;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,10:31:99:295,0,742
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|
|
3059 chr1 124134 . C T 690.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.024;DP=29;Dels=0.00;FS=10.056;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=3.001;QD=23.82;ReadPosRankSum=1.147;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:8,21:29:99:719,0,221
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|
|
3060 chr1 124151 . C T 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.142;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.49;MQ0=0;MQRankSum=1.104;QD=10.27;ReadPosRankSum=1.047;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:285,0,486
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|
|
3061 chr1 124152 . A G 916.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.49;MQ0=0;QD=27.62;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:945,72,0
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|
|
3062 chr1 124168 . C T 879.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.592;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=3.4667;MLEAC=2;MLEAF=1.00;MQ=42.46;MQ0=2;MQRankSum=2.281;QD=28.38;ReadPosRankSum=1.764;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,29:31:72:908,72,0
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|
|
3063 chr1 124203 . T C 759.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.72;MQ0=2;QD=25.33;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,30:30:66:788,66,0
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|
|
3064 chr1 124205 . A G 777.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.764;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.60;MQ0=2;MQRankSum=2.281;QD=25.09;ReadPosRankSum=-2.195;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,29:31:69:806,69,0
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|
|
3065 chr1 124243 . G C 675.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.16;MQ0=2;QD=28.16;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,24:24:57:704,57,0
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|
|
3066 chr1 124267 . G A 818.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.25;MQ0=0;QD=34.12;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,24:24:66:847,66,0
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|
|
3067 chr1 124277 . A C 856.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.91;MQ0=0;QD=34.27;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,25:25:69:885,69,0
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|
|
3068 chr1 124284 . C T 947.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.04;MQ0=0;QD=33.85;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,28:28:78:976,78,0
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|
|
3069 chr1 124321 . C T 993.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.624;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.37;MQ0=0;MQRankSum=2.203;QD=33.13;ReadPosRankSum=1.788;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,28:30:78:1022,78,0
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|
|
3070 chr1 124337 . C T 1115.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.315;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.29;MQ0=0;MQRankSum=2.239;QD=31.88;ReadPosRankSum=-0.107;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,33:35:90:1144,90,0
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|
|
3071 chr1 124376 . A T 778.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.420;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.24;MQ0=2;MQRankSum=1.850;QD=25.12;ReadPosRankSum=-0.645;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,29:31:66:807,66,0
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|
|
3072 chr1 124388 . C T 51.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.026;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=38.51;MQ0=0;MQRankSum=1.026;QD=12.94;ReadPosRankSum=-1.026;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,2:4:6:79,6,0
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|
|
3073 chr1 124423 . T A 12.77 LowQual AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=18.97;MQ0=9;QD=1.28;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:9,1:10:3:39,3,0
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|
|
3074 chr1 124467 . G T 1086.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.37;MQ0=10;QD=27.17;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:7,33:40:84:1115,84,0
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|
|
3075 chr1 124471 . G A 1113.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.55;MQ0=8;QD=29.31;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:7,31:38:87:1142,87,0
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|
|
3076 chr1 124494 . G A 996.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.258;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.11;MQ0=0;MQRankSum=2.064;QD=19.94;ReadPosRankSum=4.069;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:1025,0,663
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|
|
3077 chr1 124512 . A C 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.300;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.557;QD=13.28;ReadPosRankSum=1.261;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:692,0,960
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|
|
3078 chr1 124607 . T C 840.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.445;DP=50;Dels=0.00;FS=19.947;HaplotypeScore=1.6553;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.175;QD=16.82;ReadPosRankSum=1.106;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:869,0,855
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|
|
3079 chr1 124731 . C A 38.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.538;DP=30;Dels=0.00;FS=18.572;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.727;QD=1.29;ReadPosRankSum=-2.688;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,4:30:67:67,0,818
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|
|
3080 chr1 124820 . A T 638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.078;DP=48;Dels=0.00;FS=1.134;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.600;QD=13.31;ReadPosRankSum=1.683;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:667,0,918
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|
|
3081 chr1 124864 . T C 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.180;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=0.318;QD=14.06;ReadPosRankSum=-2.039;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:647,0,835
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|
|
3082 chr1 124901 . T G 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.942;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.761;QD=16.06;ReadPosRankSum=0.874;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,23:45:99:751,0,736
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|
|
3083 chr1 124917 . A T 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.090;DP=40;Dels=0.00;FS=2.784;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.79;MQ0=0;MQRankSum=0.251;QD=11.29;ReadPosRankSum=-1.145;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:480,0,891
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|
|
3084 chr1 124920 . C T 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.922;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=1.054;QD=10.47;ReadPosRankSum=-1.153;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,13:36:99:405,0,807
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|
|
3085 chr1 125002 . T C 468.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.594;DP=49;Dels=0.00;FS=1.202;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=2.069;QD=9.57;ReadPosRankSum=-1.460;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,17:49:99:497,0,1178
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|
|
3086 chr1 125004 . A G 1137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.804;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=1.148;QD=23.22;ReadPosRankSum=1.083;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,32:49:99:1166,0,460
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|
|
3087 chr1 125020 . A T 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.617;DP=46;Dels=0.00;FS=1.204;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=-1.547;QD=9.95;ReadPosRankSum=0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:486,0,1126
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|
|
3088 chr1 125046 . A G 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.163;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.20;MQ0=0;MQRankSum=1.788;QD=12.74;ReadPosRankSum=0.293;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:627,0,985
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|
|
3089 chr1 125096 . A G 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.101;DP=42;Dels=0.00;FS=1.345;HaplotypeScore=2.7212;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-1.887;QD=16.57;ReadPosRankSum=0.553;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:724,0,731
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|
|
3090 chr1 125124 . G A 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.683;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=3.985;QD=26.36;ReadPosRankSum=0.286;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:7,26:33:99:898,0,147
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|
|
3091 chr1 125126 . T C 119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.859;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=-4.029;QD=3.63;ReadPosRankSum=0.066;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,7:33:99:148,0,866
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|
|
3092 chr1 125128 . G A 86.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.228;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=-4.011;QD=2.63;ReadPosRankSum=2.370;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,7:33:99:115,0,854
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|
|
3093 chr1 125133 . C T 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.024;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=55.08;MQ0=0;MQRankSum=-3.992;QD=3.99;ReadPosRankSum=2.622;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,7:31:99:152,0,843
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|
|
3094 chr1 125134 . A G 1101.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=2;MLEAF=1.00;MQ=54.91;MQ0=0;QD=25.82;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1130,90,0
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|
|
3095 chr1 125142 . C T 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=52.83;MQ0=0;MQRankSum=4.377;QD=22.16;ReadPosRankSum=-1.254;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:10,20:30:99:693,0,230
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|
|
3096 chr1 125149 . G A 347.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=28;Dels=0.00;FS=1.690;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=50.58;MQ0=0;MQRankSum=-4.514;QD=12.42;ReadPosRankSum=0.184;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:15,13:28:99:376,0,460
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|
|
3097 chr1 125166 . C T 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=52.66;MQ0=0;MQRankSum=-4.339;QD=9.10;ReadPosRankSum=0.264;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,10:28:99:283,0,577
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|
3098 chr1 125168 . C T 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.699;DP=30;Dels=0.00;FS=1.805;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=51.84;MQ0=0;MQRankSum=4.551;QD=18.83;ReadPosRankSum=0.826;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,18:30:99:593,0,339
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|
3099 chr1 125175 . A G 1245.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=52.28;MQ0=0;QD=23.30;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1274,102,0
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|
|
3100 chr1 125190 . C T 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.418;DP=37;Dels=0.00;FS=4.233;HaplotypeScore=1.9965;MLEAC=1;MLEAF=0.500;MQ=52.15;MQ0=0;MQRankSum=-5.120;QD=10.53;ReadPosRankSum=0.820;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,15:37:99:418,0,736
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|
3101 chr1 125195 . C T 1518.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=2.9963;MLEAC=2;MLEAF=1.00;MQ=51.70;MQ0=0;QD=25.57;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1547,123,0
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|
3102 chr1 125207 . G A 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.326;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=-5.050;QD=8.99;ReadPosRankSum=2.160;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:379,0,880
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|
|
3103 chr1 125210 . C T 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.296;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=-5.050;QD=8.89;ReadPosRankSum=2.309;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:375,0,828
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|
|
3104 chr1 125216 . G C 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.307;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.26;MQ0=0;MQRankSum=-5.080;QD=8.81;ReadPosRankSum=1.918;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:372,0,862
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|
3105 chr1 125248 . T C 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.042;DP=49;Dels=0.00;FS=1.304;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=51.96;MQ0=1;MQRankSum=-3.990;QD=12.14;ReadPosRankSum=-0.686;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:623,0,932
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|
|
3106 chr1 125250 . C T 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.022;DP=47;Dels=0.00;FS=2.895;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=52.33;MQ0=1;MQRankSum=4.261;QD=18.97;ReadPosRankSum=0.245;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,27:47:99:920,0,541
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|
|
3107 chr1 125267 . T C 1345.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=1.3302;MLEAC=2;MLEAF=1.00;MQ=51.80;MQ0=1;QD=32.82;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1374,111,0
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|
3108 chr1 125269 . T C 1426.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=51.80;MQ0=1;QD=34.80;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1455,114,0
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|
3109 chr1 125274 . A T 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=49.93;MQ0=1;MQRankSum=3.553;QD=15.80;ReadPosRankSum=0.624;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:755,0,576
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|
|
3110 chr1 125306 . A T 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=36;Dels=0.00;FS=1.377;HaplotypeScore=9.9429;MLEAC=1;MLEAF=0.500;MQ=47.61;MQ0=1;MQRankSum=-2.732;QD=11.44;ReadPosRankSum=1.772;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,17:36:99:440,0,654
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|
3111 chr1 125310 . C T 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.769;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=9.9429;MLEAC=1;MLEAF=0.500;MQ=45.70;MQ0=1;MQRankSum=3.388;QD=16.64;ReadPosRankSum=-1.600;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:544,0,362
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|
|
3112 chr1 125319 . C T 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.604;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.05;MQ0=1;MQRankSum=-3.282;QD=8.96;ReadPosRankSum=2.048;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:279,0,506
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|
3113 chr1 125322 . T A 873.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.64;MQ0=1;QD=32.36;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,27:27:72:902,72,0
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|
|
3114 chr1 125330 . T A 876.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.42;MQ0=1;QD=31.31;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,28:28:72:905,72,0
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|
|
3115 chr1 125345 . C T 226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.830;DP=23;Dels=0.00;FS=1.740;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.96;MQ0=0;MQRankSum=-3.132;QD=9.86;ReadPosRankSum=-0.031;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:255,0,427
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|
3116 chr1 125408 . C T 195.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.01;MQ0=0;QD=32.64;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:224,18,0
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|
|
3117 chr1 125409 . C G 191.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.01;MQ0=0;QD=31.97;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:220,18,0
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|
|
3118 chr1 125410 . C G 194.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.01;MQ0=0;QD=32.47;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:223,18,0
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|
3119 chr1 125416 . G T 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.456;DP=14;Dels=0.00;FS=2.963;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.55;MQ0=0;MQRankSum=1.734;QD=1.00;ReadPosRankSum=-0.822;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,2:14:42:42,0,418
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3120 chr1 125441 . A G 103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.742;DP=24;Dels=0.00;FS=1.760;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=1;MQRankSum=-3.324;QD=4.32;ReadPosRankSum=-3.905;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:15,9:24:99:132,0,545
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|
3121 chr1 125444 . C T 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.594;DP=26;Dels=0.00;FS=1.697;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.30;MQ0=1;MQRankSum=3.652;QD=21.11;ReadPosRankSum=2.746;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:10,16:26:99:577,0,160
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|
3122 chr1 125447 . G A 146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.535;DP=24;Dels=0.00;FS=1.744;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.32;MQ0=1;MQRankSum=-3.937;QD=6.12;ReadPosRankSum=-2.551;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:175,0,501
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3123 chr1 125453 . G A 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.271;DP=24;Dels=0.00;FS=3.963;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.60;MQ0=1;MQRankSum=-4.062;QD=7.91;ReadPosRankSum=-2.946;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,11:24:99:218,0,462
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|
3124 chr1 125481 . A G 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.995;DP=33;Dels=0.00;FS=3.256;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.76;MQ0=1;MQRankSum=-4.758;QD=8.93;ReadPosRankSum=2.724;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:323,0,666
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3125 chr1 125491 . G C 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.934;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.31;ReadPosRankSum=1.104;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:286,0,566
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|
3126 chr1 125495 . G A 260.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.953;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.43;ReadPosRankSum=1.161;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:289,0,560
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3127 chr1 125497 . A G 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.689;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.55;ReadPosRankSum=1.274;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:292,0,557
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3128 chr1 125498 . C T 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.425;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.19;ReadPosRankSum=1.387;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:283,0,571
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3129 chr1 125503 . A G 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.671;DP=26;Dels=0.00;FS=1.657;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.08;MQ0=0;MQRankSum=-4.042;QD=10.14;ReadPosRankSum=1.294;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,9:26:99:292,0,609
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3130 chr1 125509 . C T 1210.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.00;MQ0=0;QD=28.40;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1239,93,0
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3131 chr1 125530 . T C 1192.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.61;MQ0=0;QD=25.52;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1221,93,0
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3132 chr1 125548 . C A 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.637;DP=29;Dels=0.00;FS=9.640;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=2.073;QD=16.13;ReadPosRankSum=0.153;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,15:29:99:496,0,417
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|
3133 chr1 125550 . G A 1067.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=57.16;MQ0=0;QD=31.72;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1096,87,0
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|
3134 chr1 125582 . C T 590.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.929;DP=28;Dels=0.00;FS=3.771;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=1;MQRankSum=0.386;QD=21.10;ReadPosRankSum=-0.849;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:10,18:28:99:619,0,268
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3135 chr1 125589 . A T 672.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.41;MQ0=0;QD=28.99;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,18:18:51:701,51,0
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|
3136 chr1 125622 . A C 808.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.336;DP=42;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=1;MQRankSum=-0.542;QD=19.26;ReadPosRankSum=-0.251;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:837,0,537
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|
3137 chr1 125640 . G T 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.195;DP=41;Dels=0.00;FS=2.681;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=-1.405;QD=14.29;ReadPosRankSum=3.533;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:614,0,776
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|
3138 chr1 125691 . C T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.118;DP=44;Dels=0.00;FS=4.165;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=0;MQRankSum=-2.085;QD=13.79;ReadPosRankSum=-0.308;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,19:44:99:635,0,863
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3139 chr1 125721 . T G 219.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=36;Dels=0.00;FS=1.512;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=0;MQRankSum=-1.754;QD=6.10;ReadPosRankSum=0.913;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,9:36:99:248,0,910
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3140 chr1 125736 . T C 235.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.326;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=-1.023;QD=7.61;ReadPosRankSum=-0.457;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,9:31:99:264,0,762
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3141 chr1 125740 . A G 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.306;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=58.25;MQ0=0;MQRankSum=-1.249;QD=8.20;ReadPosRankSum=-1.014;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,9:29:99:266,0,653
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3142 chr1 125759 . T C 320.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.697;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=-3.079;QD=11.06;ReadPosRankSum=-0.652;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,11:29:99:349,0,542
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3143 chr1 125772 . C G 360.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.466;DP=26;Dels=0.00;FS=8.852;HaplotypeScore=17.6766;MLEAC=1;MLEAF=0.500;MQ=55.71;MQ0=0;MQRankSum=-4.089;QD=13.88;ReadPosRankSum=-0.489;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,12:26:99:389,0,400
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3144 chr1 125787 . G T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.380;DP=26;Dels=0.00;FS=12.825;HaplotypeScore=2.9982;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=1.463;QD=0.57;ReadPosRankSum=-2.801;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,3:26:43:43,0,723
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3145 chr1 125794 . C T 310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.246;DP=25;Dels=0.00;FS=1.697;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.49;MQ0=0;MQRankSum=-4.243;QD=12.43;ReadPosRankSum=1.670;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,11:25:99:339,0,466
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3146 chr1 125810 . G T 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.755;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-4.808;QD=9.17;ReadPosRankSum=1.750;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,13:33:99:331,0,680
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3147 chr1 125834 . T G 1147.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.621;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.7719;MLEAC=2;MLEAF=1.00;MQ=58.76;MQ0=0;MQRankSum=-0.503;QD=26.31;ReadPosRankSum=-1.286;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:1,30:31:70:1176,70,0
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3148 chr1 126025 . G A 1160.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=54.1245;MLEAC=2;MLEAF=1.00;MQ=47.94;MQ0=0;QD=26.85;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1189,90,0
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3149 chr1 126059 . T C 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.273;DP=34;Dels=0.00;FS=7.712;HaplotypeScore=13.5642;MLEAC=1;MLEAF=0.500;MQ=46.49;MQ0=0;MQRankSum=4.960;QD=16.52;ReadPosRankSum=-2.721;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:590,0,540
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3150 chr1 126061 . T A 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.514;DP=34;Dels=0.00;FS=7.712;HaplotypeScore=13.5642;MLEAC=1;MLEAF=0.500;MQ=46.49;MQ0=0;MQRankSum=4.960;QD=16.40;ReadPosRankSum=-3.341;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:586,0,522
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3151 chr1 126072 . G A 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.927;DP=28;Dels=0.00;FS=6.029;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.25;MQ0=0;MQRankSum=-4.480;QD=11.53;ReadPosRankSum=1.648;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:351,0,542
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3152 chr1 126082 . A T 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.310;DP=19;Dels=0.00;FS=7.701;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.40;MQ0=0;MQRankSum=-3.592;QD=9.46;ReadPosRankSum=1.479;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,7:19:99:208,0,430
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3153 chr1 126524 . G A 622.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.36;MQ0=0;QD=27.99;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:651,51,0
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3154 chr1 126529 . T A 646.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.36;MQ0=0;QD=27.13;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:675,51,0
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3155 chr1 126531 . C T 649.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.36;MQ0=0;QD=30.09;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:678,51,0
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3156 chr1 126536 . G A 653.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.36;MQ0=0;QD=25.84;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:682,51,0
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3157 chr1 126547 . G A 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.082;DP=25;Dels=0.00;FS=13.262;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=47.44;MQ0=0;MQRankSum=0.082;QD=16.95;ReadPosRankSum=4.215;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,13:25:99:452,0,359
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3158 chr1 126551 . A G 380.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.496;DP=25;Dels=0.00;FS=13.829;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=48.34;MQ0=0;MQRankSum=0.027;QD=15.23;ReadPosRankSum=4.215;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,12:25:99:409,0,391
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3159 chr1 126556 . T C 297.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.263;DP=24;Dels=0.00;FS=26.945;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.95;MQ0=0;MQRankSum=-0.381;QD=12.41;ReadPosRankSum=4.070;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:326,0,444
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3160 chr1 126572 . G C 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.553;DP=49;Dels=0.00;FS=4.366;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=49.66;MQ0=0;MQRankSum=-3.829;QD=8.40;ReadPosRankSum=0.618;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:34,15:49:99:440,0,1091
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3161 chr1 126583 . C T 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.466;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=12.9923;MLEAC=1;MLEAF=0.500;MQ=50.69;MQ0=0;MQRankSum=-1.853;QD=19.55;ReadPosRankSum=5.365;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,28:47:99:947,0,591
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3162 chr1 126584 . G A 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.103;DP=47;Dels=0.00;FS=2.763;HaplotypeScore=12.9923;MLEAC=1;MLEAF=0.500;MQ=50.69;MQ0=0;MQRankSum=-4.028;QD=8.53;ReadPosRankSum=1.677;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,15:47:99:429,0,1116
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3163 chr1 126595 . A T 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.488;DP=52;Dels=0.00;FS=2.606;HaplotypeScore=22.9737;MLEAC=1;MLEAF=0.500;MQ=51.73;MQ0=0;MQRankSum=-4.709;QD=8.67;ReadPosRankSum=2.092;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,16:52:99:479,0,1271
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3164 chr1 126599 . G T 1355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.510;DP=50;Dels=0.00;FS=1.289;HaplotypeScore=32.9690;MLEAC=1;MLEAF=0.500;MQ=52.25;MQ0=0;MQRankSum=-2.510;QD=27.12;ReadPosRankSum=-1.715;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,38:50:99:1384,0,313
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3165 chr1 126603 . A G 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;DP=50;Dels=0.00;FS=2.527;HaplotypeScore=32.7034;MLEAC=1;MLEAF=0.500;MQ=52.38;MQ0=0;MQRankSum=-4.690;QD=8.90;ReadPosRankSum=4.066;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:34,16:50:99:473,0,1206
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|
|
3166 chr1 126605 . C T 779.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.085;DP=51;Dels=0.00;FS=2.369;HaplotypeScore=32.7046;MLEAC=1;MLEAF=0.500;MQ=52.54;MQ0=0;MQRankSum=3.501;QD=15.29;ReadPosRankSum=-4.331;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:808,0,893
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|
3167 chr1 126609 . C T 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.515;DP=50;Dels=0.00;FS=2.429;HaplotypeScore=30.7052;MLEAC=1;MLEAF=0.500;MQ=52.80;MQ0=0;MQRankSum=-2.243;QD=17.32;ReadPosRankSum=3.641;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,26:50:99:894,0,800
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|
|
3168 chr1 126615 . T A 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.333;DP=53;Dels=0.00;FS=8.297;HaplotypeScore=11.7855;MLEAC=1;MLEAF=0.500;MQ=54.30;MQ0=0;MQRankSum=-5.840;QD=8.94;ReadPosRankSum=4.602;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,17:53:99:502,0,1303
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|
|
3169 chr1 126645 . G A 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.957;DP=65;Dels=0.00;FS=13.603;HaplotypeScore=100.5169;MLEAC=1;MLEAF=0.500;MQ=55.52;MQ0=0;MQRankSum=-5.977;QD=5.77;ReadPosRankSum=-1.607;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:49,16:65:99:403,0,1747
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|
|
3170 chr1 126670 . C T 634.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.047;DP=54;Dels=0.00;FS=1.105;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-1.100;QD=11.75;ReadPosRankSum=-0.710;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:33,21:54:99:663,0,1180
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|
|
3171 chr1 126698 . T C 1233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.857;DP=55;Dels=0.00;FS=8.472;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=2.036;QD=22.43;ReadPosRankSum=2.161;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,37:55:99:1262,0,539
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|
|
3172 chr1 126702 . T C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.824;DP=58;Dels=0.00;FS=16.756;HaplotypeScore=5.9982;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=-0.515;QD=9.98;ReadPosRankSum=-2.609;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:38,20:58:99:607,0,1364
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|
|
3173 chr1 126709 . C T 292.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.843;DP=54;Dels=0.00;FS=4.827;HaplotypeScore=4.9981;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=0.447;QD=5.42;ReadPosRankSum=-0.697;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:42,12:54:99:321,0,1519
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|
|
3174 chr1 126712 . A T 2169.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=9.9949;MLEAC=2;MLEAF=1.00;MQ=59.76;MQ0=0;QD=27.57;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2198,166,0
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|
|
3175 chr1 126725 . G T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.205;DP=57;Dels=0.00;FS=9.993;HaplotypeScore=9.9931;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=1.729;QD=12.00;ReadPosRankSum=-1.418;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:35,22:57:99:712,0,1228
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|
|
3176 chr1 126730 . T C 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.295;DP=53;Dels=0.00;FS=6.032;HaplotypeScore=9.9931;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=0.467;QD=9.18;ReadPosRankSum=-2.601;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,17:53:99:515,0,1208
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|
3177 chr1 126761 . C A 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.830;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=2.9989;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=1.910;QD=16.77;ReadPosRankSum=-0.350;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:850,0,808
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|
3178 chr1 126795 . T A 1211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.494;DP=58;Dels=0.00;FS=1.054;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=-1.462;QD=20.89;ReadPosRankSum=1.685;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,35:58:99:1240,0,735
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|
|
3179 chr1 126808 . C T 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.677;DP=61;Dels=0.00;FS=3.491;HaplotypeScore=16.9835;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=-3.792;QD=1.68;ReadPosRankSum=-0.502;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:53,8:61:99:131,0,1927
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|
|
3180 chr1 126813 . C A 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.396;DP=62;Dels=0.00;FS=3.493;HaplotypeScore=46.9121;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-3.433;QD=1.59;ReadPosRankSum=0.304;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:54,8:62:99:127,0,1961
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|
3181 chr1 126818 . A T 1188.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.396;DP=60;Dels=0.00;FS=3.656;HaplotypeScore=46.9121;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=-1.381;QD=19.81;ReadPosRankSum=-0.083;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,36:60:99:1217,0,765
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|
3182 chr1 126828 . G A 1176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.847;DP=64;Dels=0.00;FS=3.468;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.035;QD=18.39;ReadPosRankSum=0.616;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,36:64:99:1205,0,913
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|
3183 chr1 126853 . C T 183.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.453;DP=65;Dels=0.00;FS=24.367;HaplotypeScore=18.9957;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=1;MQRankSum=-2.099;QD=2.83;ReadPosRankSum=-0.102;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:54,11:65:99:212,0,1982
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|
3184 chr1 126860 . A C 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.719;DP=68;Dels=0.00;FS=20.308;HaplotypeScore=26.9946;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=1;MQRankSum=-1.259;QD=2.08;ReadPosRankSum=0.450;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:58,10:68:99:170,0,2073
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|
3185 chr1 126861 . T A 1035.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.510;DP=69;Dels=0.00;FS=6.505;HaplotypeScore=26.9946;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=1;MQRankSum=0.043;QD=15.01;ReadPosRankSum=1.333;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,33:69:99:1064,0,1239
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|
3186 chr1 126865 . G C 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.017;DP=69;Dels=0.00;FS=24.072;HaplotypeScore=18.9966;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=1;MQRankSum=-0.684;QD=2.62;ReadPosRankSum=0.043;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:58,11:69:99:209,0,2116
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|
3187 chr1 126883 . A G 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.091;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=1;MQRankSum=0.724;QD=7.50;ReadPosRankSum=0.943;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:50,19:69:99:546,0,1802
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3188 chr1 126896 . G T 1175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.676;DP=66;Dels=0.00;FS=6.828;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=1;MQRankSum=0.099;QD=17.81;ReadPosRankSum=-1.057;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1204,0,1011
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|
3189 chr1 126923 . A G 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=68;Dels=0.00;FS=11.174;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=1;MQRankSum=1.555;QD=9.54;ReadPosRankSum=-1.395;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:46,22:68:99:677,0,1574
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|
3190 chr1 126945 . A T 301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.121;DP=63;Dels=0.00;FS=9.115;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=1;MQRankSum=0.380;QD=4.79;ReadPosRankSum=0.847;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:49,14:63:99:330,0,1740
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|
3191 chr1 126957 . C T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.697;DP=59;Dels=0.00;FS=5.370;HaplotypeScore=18.9933;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=1;MQRankSum=0.773;QD=2.47;ReadPosRankSum=1.289;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:49,10:59:99:174,0,1767
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|
3192 chr1 126959 . A G 174.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=55;Dels=0.00;FS=5.678;HaplotypeScore=18.9933;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=1;MQRankSum=-0.116;QD=3.18;ReadPosRankSum=0.812;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:45,10:55:99:203,0,1601
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|
3193 chr1 126963 . C A 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.904;DP=54;Dels=0.00;FS=19.876;HaplotypeScore=17.9934;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=1;MQRankSum=-0.135;QD=13.01;ReadPosRankSum=0.695;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:731,0,1059
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3194 chr1 126974 . G A 1026.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.932;DP=53;Dels=0.00;FS=4.336;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.77;MQ0=1;MQRankSum=-0.448;QD=19.37;ReadPosRankSum=-0.858;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,32:53:99:1055,0,636
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|
3195 chr1 126988 . T C 66.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.408;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.09;MQ0=1;MQRankSum=-0.179;QD=1.42;ReadPosRankSum=-0.636;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:40,7:47:95:95,0,1426
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3196 chr1 127068 . T C 919.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.25;MQ0=0;QD=27.97;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:948,72,0
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3197 chr1 127210 . C G 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.118;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=1.8245;MLEAC=1;MLEAF=0.500;MQ=53.31;MQ0=0;MQRankSum=1.532;QD=1.71;ReadPosRankSum=-1.296;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:9,2:11:47:47,0,276
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3198 chr1 127231 . C A 235.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.94;MQ0=0;QD=33.69;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:264,21,0
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3199 chr1 127271 . G A 273.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.262;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.35;MQ0=0;MQRankSum=2.262;QD=24.89;ReadPosRankSum=0.566;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:3,8:11:24:302,24,0
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3200 chr1 127280 . C T 285.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=38.63;MQ0=2;QD=23.82;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,12:12:24:314,24,0
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3201 chr1 127338 . C T 75.03 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;DP=5;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.92;MQ0=0;MQRankSum=0.731;QD=15.01;ReadPosRankSum=0.731;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:1,4:5:12:103,0,12
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3202 chr1 127348 . G A 75.03 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;DP=6;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.23;MQ0=0;MQRankSum=0.720;QD=12.51;ReadPosRankSum=1.380;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:2,4:6:12:103,0,12
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3203 chr1 127382 . C T 90.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.568;DP=10;Dels=0.00;FS=11.181;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=35.14;MQ0=0;MQRankSum=2.383;QD=9.08;ReadPosRankSum=-0.741;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:6,4:10:43:119,0,43
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3204 chr1 127438 . G T 310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.401;DP=27;Dels=0.00;FS=15.441;HaplotypeScore=6.0290;MLEAC=1;MLEAF=0.500;MQ=25.45;MQ0=5;MQRankSum=2.404;QD=11.51;ReadPosRankSum=1.469;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,14:27:56:339,0,56
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3205 chr1 127457 . C T 504.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.419;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=4.1428;MLEAC=2;MLEAF=1.00;MQ=26.11;MQ0=5;MQRankSum=0.959;QD=18.03;ReadPosRankSum=0.228;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:5,23:28:51:533,51,0
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3206 chr1 127490 . G A 323.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.000;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.41;MQ0=1;MQRankSum=1.488;QD=21.58;ReadPosRankSum=1.240;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:1,14:15:36:352,36,0
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3207 chr1 127515 . T C 221.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.49;MQ0=0;QD=24.64;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,9:9:24:250,24,0
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3208 chr1 127567 . G A 69.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.897;DP=35;Dels=0.00;FS=6.623;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=43.19;MQ0=2;MQRankSum=-4.564;QD=1.99;ReadPosRankSum=-3.380;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,12:35:98:98,0,737
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3209 chr1 127579 . G C 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=39;Dels=0.00;FS=3.519;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.40;MQ0=2;MQRankSum=-4.786;QD=2.30;ReadPosRankSum=-2.028;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:118,0,827
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3210 chr1 127590 . A G 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.015;DP=42;Dels=0.00;FS=4.107;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.59;MQ0=2;MQRankSum=-4.885;QD=1.95;ReadPosRankSum=1.048;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:29,13:42:99:110,0,969
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|
3211 chr1 127595 . T G 1307.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.28;MQ0=2;QD=29.72;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1336,111,0
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|
|
3212 chr1 127637 . A G 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.819;DP=40;Dels=0.00;FS=12.746;HaplotypeScore=2.4098;MLEAC=1;MLEAF=0.500;MQ=51.13;MQ0=0;MQRankSum=-4.973;QD=2.04;ReadPosRankSum=-1.284;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,12:40:99:110,0,984
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|
3213 chr1 127648 . G A 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.114;DP=35;Dels=0.00;FS=12.225;HaplotypeScore=1.8110;MLEAC=1;MLEAF=0.500;MQ=52.90;MQ0=0;MQRankSum=4.397;QD=25.96;ReadPosRankSum=3.076;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:9,26:35:99:937,0,111
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|
3214 chr1 127656 . T C 1057.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.13;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1086,81,0
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|
3215 chr1 127661 . C T 1052.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.96;MQ0=0;QD=32.43;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1081,81,0
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|
3216 chr1 127677 . T C 998.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.78;MQ0=0;QD=30.02;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,25:27:75:1027,75,0
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|
3217 chr1 127909 . T A 404.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.68;MQ0=5;QD=19.27;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,21:21:42:433,42,0
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|
3218 chr1 127922 . T C 479.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.69;MQ0=4;QD=22.85;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,21:21:45:508,45,0
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|
|
3219 chr1 127948 . A G 614.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.18;MQ0=4;QD=26.73;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,23:23:51:643,51,0
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|
|
3220 chr1 128047 . A G 823.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.02;MQ0=1;QD=29.22;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q26|Cc01g00090|mRNA||GSCOCT00012429001|Exon_chr1_127970_128260) GT:AD:DP:GQ:PL 1/1:0,23:23:63:852,63,0
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|
|
3221 chr1 128090 . A T 825.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.66;MQ0=1;QD=25.81;EFF=STOP_GAINED(HIGH|NONSENSE|Aga/Tga|R41*|Cc01g00090|mRNA||GSCOCT00012429001|Exon_chr1_127970_128260) GT:AD:DP:GQ:PL 1/1:0,32:32:69:854,69,0
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|
3222 chr1 128144 . C T 1024.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.67;MQ0=0;QD=31.05;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L59|Cc01g00090|mRNA||GSCOCT00012429001|Exon_chr1_127970_128260) GT:AD:DP:GQ:PL 1/1:0,33:33:81:1053,81,0
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|
3223 chr1 128315 . C T 802.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.9967;MLEAC=2;MLEAF=1.00;MQ=57.38;MQ0=0;QD=29.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,22:22:63:831,63,0
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3224 chr1 128373 . T A 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.675;DP=31;Dels=0.00;FS=10.328;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.35;MQ0=0;MQRankSum=-3.475;QD=1.64;ReadPosRankSum=-1.875;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,6:31:79:79,0,886
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|
3225 chr1 128434 . A G 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.517;DP=34;Dels=0.00;FS=10.976;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.34;MQ0=0;MQRankSum=-4.271;QD=13.76;ReadPosRankSum=1.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:496,0,567
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3226 chr1 128435 . C A 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.620;DP=34;Dels=0.00;FS=13.315;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.34;MQ0=0;MQRankSum=4.202;QD=15.61;ReadPosRankSum=-1.929;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:559,0,495
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3227 chr1 128484 . G A 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.879;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-4.478;QD=17.06;ReadPosRankSum=0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:540,0,432
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3228 chr1 128493 . A G 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.428;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.90;MQ0=0;MQRankSum=-4.008;QD=15.96;ReadPosRankSum=0.507;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:13,15:28:99:475,0,439
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|
3229 chr1 128534 . G T 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=28;Dels=0.00;FS=5.632;HaplotypeScore=18.3580;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=0.821;QD=1.99;ReadPosRankSum=-2.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:24,4:28:84:84,0,841
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3230 chr1 128588 . C T 661.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=37;Dels=0.00;FS=28.800;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;MQRankSum=-0.381;QD=17.89;ReadPosRankSum=1.356;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:690,0,561
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3231 chr1 128665 . A G 1175.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.03;FS=0.000;HaplotypeScore=3.2953;MLEAC=2;MLEAF=1.00;MQ=59.42;MQ0=0;QD=33.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1204,93,0
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|
3232 chr1 128691 . G A 259.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.043;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=4;MQRankSum=-0.764;QD=6.66;ReadPosRankSum=-0.657;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:28,11:39:99:288,0,846
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3233 chr1 128700 . T C 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.370;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.10;MQ0=5;MQRankSum=-1.458;QD=4.21;ReadPosRankSum=-0.152;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:184,0,862
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3234 chr1 128703 . A G 146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.686;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.40;MQ0=5;MQRankSum=-0.441;QD=4.19;ReadPosRankSum=-0.049;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:28,7:35:99:175,0,799
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|
|
3235 chr1 128705 . C T 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.535;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.53;MQ0=5;MQRankSum=-0.969;QD=4.27;ReadPosRankSum=0.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:29,7:36:99:182,0,890
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3236 chr1 128706 . A G 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.275;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.40;MQ0=5;MQRankSum=-1.471;QD=4.59;ReadPosRankSum=0.049;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:28,7:35:99:189,0,851
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3237 chr1 128741 . T C 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.822;DP=49;Dels=0.00;FS=18.338;HaplotypeScore=2.9979;MLEAC=1;MLEAF=0.500;MQ=54.84;MQ0=3;MQRankSum=-1.889;QD=10.67;ReadPosRankSum=2.025;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:551,0,903
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3238 chr1 128751 . A G 516.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.379;DP=53;Dels=0.00;FS=22.251;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=55.24;MQ0=3;MQRankSum=-1.700;QD=9.75;ReadPosRankSum=3.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:34,19:53:99:545,0,1055
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3239 chr1 128795 . G A 820.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.675;DP=55;Dels=0.00;FS=5.871;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=-3.881;QD=14.92;ReadPosRankSum=-1.456;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:849,0,927
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|
3240 chr1 128807 . T C 738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.729;DP=57;Dels=0.00;FS=5.835;HaplotypeScore=10.9974;MLEAC=1;MLEAF=0.500;MQ=56.07;MQ0=0;MQRankSum=-3.485;QD=12.96;ReadPosRankSum=3.212;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:767,0,1052
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|
3241 chr1 128808 . C T 2130.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=11.9972;MLEAC=2;MLEAF=1.00;MQ=56.00;MQ0=0;QD=30.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2159,165,0
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|
|
3242 chr1 128816 . A G 299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.629;DP=56;Dels=0.00;FS=11.033;HaplotypeScore=23.9742;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=0.409;QD=5.35;ReadPosRankSum=-2.905;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:44,12:56:99:328,0,1466
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3243 chr1 128821 . G T 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.263;DP=54;Dels=0.00;FS=1.128;HaplotypeScore=13.9934;MLEAC=1;MLEAF=0.500;MQ=56.41;MQ0=0;MQRankSum=-1.961;QD=19.50;ReadPosRankSum=3.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,34:54:99:1081,0,641
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|
3244 chr1 128823 . C T 952.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.196;DP=51;Dels=0.00;FS=1.146;HaplotypeScore=22.8239;MLEAC=1;MLEAF=0.500;MQ=57.23;MQ0=0;MQRankSum=-0.718;QD=18.68;ReadPosRankSum=2.727;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:21,30:51:99:981,0,699
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|
|
3245 chr1 128833 . C T 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.443;DP=53;Dels=0.00;FS=6.025;HaplotypeScore=10.8296;MLEAC=1;MLEAF=0.500;MQ=57.48;MQ0=0;MQRankSum=-0.580;QD=3.51;ReadPosRankSum=0.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:43,10:53:99:214,0,1479
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|
|
3246 chr1 128853 . G A 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.528;DP=49;Dels=0.00;FS=11.665;HaplotypeScore=1.6634;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=0;MQRankSum=-1.294;QD=3.67;ReadPosRankSum=1.902;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:39,9:49:99:208,0,1382
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|
|
3247 chr1 128899 . G A 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.178;DP=38;Dels=0.00;FS=4.943;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=0;MQRankSum=-3.084;QD=11.84;ReadPosRankSum=-1.213;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:478,0,618
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|
|
3248 chr1 128911 . T C 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.951;DP=51;Dels=0.00;FS=1.395;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-2.607;QD=3.39;ReadPosRankSum=-3.817;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:42,9:51:99:201,0,1364
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|
|
3249 chr1 128916 . G A 173.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.605;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.91;MQ0=0;MQRankSum=-1.816;QD=3.41;ReadPosRankSum=-2.706;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:42,9:51:99:202,0,1455
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|
|
3250 chr1 128946 . A G 568.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.281;DP=60;Dels=0.00;FS=2.267;HaplotypeScore=13.9962;MLEAC=1;MLEAF=0.500;MQ=56.81;MQ0=0;MQRankSum=-1.741;QD=9.48;ReadPosRankSum=1.787;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:38,22:60:99:597,0,1331
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|
|
3251 chr1 128948 . A C 588.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.669;DP=62;Dels=0.00;FS=1.018;HaplotypeScore=31.9736;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=0;MQRankSum=-2.302;QD=9.50;ReadPosRankSum=1.640;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:40,22:62:99:617,0,1424
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|
|
3252 chr1 128956 . C G 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.709;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=47.9525;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=0.097;QD=7.15;ReadPosRankSum=1.620;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:493,0,1642
|
|
|
3253 chr1 128957 . T G 1312.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=63;Dels=0.00;FS=2.198;HaplotypeScore=33.9668;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-1.149;QD=20.84;ReadPosRankSum=1.949;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:23,40:63:99:1341,0,755
|
|
|
3254 chr1 128961 . G A 1257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=63;Dels=0.00;FS=2.198;HaplotypeScore=17.9912;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-1.577;QD=19.96;ReadPosRankSum=1.877;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:23,40:63:99:1286,0,756
|
|
|
3255 chr1 128975 . G T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.259;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=33.8278;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=-0.350;QD=10.39;ReadPosRankSum=-0.311;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:45,23:68:99:735,0,1596
|
|
|
3256 chr1 128988 . G A 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.066;DP=73;Dels=0.00;FS=12.861;HaplotypeScore=23.3284;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=-0.345;QD=5.52;ReadPosRankSum=1.976;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:55,17:73:99:431,0,2010
|
|
|
3257 chr1 129160 . A T 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.395;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=53.02;MQ0=0;MQRankSum=-5.688;QD=4.52;ReadPosRankSum=-1.880;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:48,15:63:99:313,0,1702
|
|
|
3258 chr1 129165 . G T 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.047;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-5.619;QD=4.83;ReadPosRankSum=-1.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:46,15:61:99:323,0,1605
|
|
|
3259 chr1 129168 . A G 291.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.381;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=52.55;MQ0=0;MQRankSum=-5.671;QD=4.71;ReadPosRankSum=-0.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:47,15:62:99:320,0,1616
|
|
|
3260 chr1 129170 . G T 2364.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.46;MQ0=0;QD=33.61;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2393,187,0
|
|
|
3261 chr1 129174 . T A 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.686;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.87;MQ0=0;MQRankSum=-5.798;QD=4.36;ReadPosRankSum=1.384;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:50,16:66:99:316,0,1690
|
|
|
3262 chr1 129186 . A C 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.619;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQ0=1;MQRankSum=-6.469;QD=6.53;ReadPosRankSum=1.121;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:46,23:69:99:479,0,1553
|
|
|
3263 chr1 129201 . C T 325.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.234;DP=58;Dels=0.00;FS=2.756;HaplotypeScore=12.9038;MLEAC=1;MLEAF=0.500;MQ=49.38;MQ0=1;MQRankSum=1.307;QD=5.62;ReadPosRankSum=1.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:44,14:58:99:354,0,1347
|
|
|
3264 chr1 129215 . C A 458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.088;DP=44;Dels=0.00;FS=1.218;HaplotypeScore=9.9234;MLEAC=1;MLEAF=0.500;MQ=51.67;MQ0=1;MQRankSum=-4.732;QD=10.43;ReadPosRankSum=1.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:487,0,829
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|
|
3265 chr1 129227 . T C 170.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=2.3660;MLEAC=1;MLEAF=0.500;MQ=52.06;MQ0=1;MQRankSum=-4.330;QD=5.34;ReadPosRankSum=1.719;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:199,0,742
|
|
|
3266 chr1 129279 . T G 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.257;DP=43;Dels=0.00;FS=7.514;HaplotypeScore=1.9990;MLEAC=1;MLEAF=0.500;MQ=55.76;MQ0=2;MQRankSum=-0.257;QD=20.27;ReadPosRankSum=-4.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:15,28:43:99:900,0,484
|
|
|
3267 chr1 129287 . G A 991.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.143;DP=45;Dels=0.00;FS=10.631;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=55.96;MQ0=2;MQRankSum=-1.076;QD=22.04;ReadPosRankSum=-3.486;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:14,31:45:99:1020,0,440
|
|
|
3268 chr1 129320 . T A 1123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.339;DP=51;Dels=0.00;FS=20.436;HaplotypeScore=2.9997;MLEAC=1;MLEAF=0.500;MQ=57.21;MQ0=3;MQRankSum=0.864;QD=22.03;ReadPosRankSum=3.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,34:51:99:1152,0,502
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|
|
3269 chr1 129323 . A G 1012.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.889;DP=48;Dels=0.00;FS=17.838;HaplotypeScore=3.9996;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=3;MQRankSum=0.605;QD=21.10;ReadPosRankSum=3.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,31:48:99:1041,0,518
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|
|
3270 chr1 129341 . C G 186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.334;DP=57;Dels=0.00;FS=17.030;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=6;MQRankSum=-1.618;QD=3.28;ReadPosRankSum=-3.842;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:43,14:57:99:215,0,1547
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|
|
3271 chr1 129364 . G A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.104;DP=53;Dels=0.00;FS=30.019;HaplotypeScore=14.7852;MLEAC=1;MLEAF=0.500;MQ=56.85;MQ0=5;MQRankSum=-1.619;QD=5.17;ReadPosRankSum=0.392;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:37,16:53:99:302,0,1331
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|
|
3272 chr1 129366 . C T 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.951;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=12.7857;MLEAC=1;MLEAF=0.500;MQ=56.79;MQ0=5;MQRankSum=2.207;QD=16.03;ReadPosRankSum=-0.714;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:862,0,729
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|
|
3273 chr1 129393 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.105;DP=49;Dels=0.00;FS=6.439;HaplotypeScore=51.4904;MLEAC=1;MLEAF=0.500;MQ=57.40;MQ0=1;MQRankSum=-1.665;QD=10.87;ReadPosRankSum=1.560;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:29,20:49:99:561,0,1020
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|
|
3274 chr1 129409 . C T 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.755;DP=52;Dels=0.00;FS=15.514;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=1;MQRankSum=-1.292;QD=7.01;ReadPosRankSum=2.326;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:36,16:52:99:393,0,1247
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|
|
3275 chr1 129415 . T G 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.131;DP=49;Dels=0.00;FS=10.402;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=1;MQRankSum=-1.083;QD=4.57;ReadPosRankSum=1.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:36,13:49:99:252,0,1255
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|
|
3276 chr1 129421 . A G 204.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.641;DP=47;Dels=0.00;FS=10.402;HaplotypeScore=14.7307;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-0.163;QD=4.36;ReadPosRankSum=1.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:36,11:47:99:233,0,1272
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|
|
3277 chr1 129428 . T A 80.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.961;DP=47;Dels=0.00;FS=11.605;HaplotypeScore=14.5195;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=0.749;QD=1.72;ReadPosRankSum=0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:41,6:47:99:109,0,1365
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|
|
3278 chr1 129430 . T C 1335.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.868;DP=47;Dels=0.00;FS=14.700;HaplotypeScore=13.5208;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-0.941;QD=28.42;ReadPosRankSum=-1.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:7,40:47:99:1364,0,151
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|
|
3279 chr1 129470 . A G 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.482;DP=34;Dels=0.00;FS=6.431;HaplotypeScore=3.9295;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=3.106;QD=26.23;ReadPosRankSum=3.268;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:8,26:34:99:920,0,161
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|
|
3280 chr1 129498 . G A 174.9 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.78;MQ0=0;QD=29.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,6:6:15:203,15,0
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|
|
3281 chr1 129499 . G A 154.94 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;DP=6;Dels=0.00;FS=4.771;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.78;MQ0=0;MQRankSum=0.736;QD=25.82;ReadPosRankSum=0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:1,5:6:14:183,0,14
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|
|
3282 chr1 129592 . A G 656.9 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.867;DP=20;Dels=0.00;FS=9.777;HaplotypeScore=22.2964;MLEAC=2;MLEAF=1.00;MQ=53.98;MQ0=0;MQRankSum=-1.387;QD=32.85;ReadPosRankSum=-1.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:1,19:20:15:685,15,0
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|
|
3283 chr1 129600 . G A 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.156;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=2.9992;MLEAC=1;MLEAF=0.500;MQ=53.77;MQ0=0;MQRankSum=1.557;QD=13.22;ReadPosRankSum=-0.519;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:15,11:26:99:372,0,498
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|
|
3284 chr1 129610 . G T 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.411;DP=28;Dels=0.00;FS=28.641;HaplotypeScore=3.7875;MLEAC=1;MLEAF=0.500;MQ=54.24;MQ0=0;MQRankSum=-2.006;QD=30.10;ReadPosRankSum=0.446;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:3,25:28:36:871,0,36
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|
|
3285 chr1 129625 . G A 379.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.306;DP=29;Dels=0.00;FS=12.308;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=56.07;MQ0=0;MQRankSum=-3.476;QD=13.10;ReadPosRankSum=1.572;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,12:29:99:408,0,556
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|
|
3286 chr1 129672 . C T 16.86 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.271;DP=10;Dels=0.00;FS=11.761;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.898;QD=1.69;ReadPosRankSum=-1.733;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:8,2:10:45:45,0,294
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|
|
3287 chr1 129688 . T C 517.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.96;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:546,42,0
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|
|
3288 chr1 129768 . T C 363.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.11;MQ0=0;QD=30.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,12:12:30:392,30,0
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|
|
3289 chr1 129773 . T C 324.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.65;MQ0=0;QD=29.53;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,11:11:27:353,27,0
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|
|
3290 chr1 129786 . T C 88.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.43;MQ0=0;QD=17.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:116,9,0
|
|
|
3291 chr1 129790 . T C 88.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.43;MQ0=0;QD=17.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:116,9,0
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3292 chr1 129791 . T A 88.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.43;MQ0=0;QD=17.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:116,9,0
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|
3293 chr1 129792 . C T 88.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.43;MQ0=0;QD=17.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:116,9,0
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|
3294 chr1 129814 . A G 86.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.45;MQ0=0;QD=17.26;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:114,9,0
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3295 chr1 129819 . A T 123.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.28;MQ0=1;QD=17.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,7:7:12:151,12,0
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3296 chr1 129823 . T C 124.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.28;MQ0=1;QD=17.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,7:7:12:152,12,0
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3297 chr1 129890 . C T 551.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.187;DP=39;Dels=0.00;FS=4.523;HaplotypeScore=2.9153;MLEAC=2;MLEAF=1.00;MQ=26.19;MQ0=13;MQRankSum=2.769;QD=14.15;ReadPosRankSum=-2.891;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:15,24:39:28:580,28,0
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|
3298 chr1 129897 . C A 631.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.036;DP=42;Dels=0.00;FS=4.559;HaplotypeScore=4.7472;MLEAC=2;MLEAF=1.00;MQ=26.06;MQ0=14;MQRankSum=2.939;QD=15.04;ReadPosRankSum=-2.715;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:18,24:42:37:660,37,0
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3299 chr1 129936 . C T 516.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.057;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.00;MQ=25.05;MQ0=5;MQRankSum=1.999;QD=19.14;ReadPosRankSum=1.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:6,21:27:48:545,48,0
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|
3300 chr1 129979 . T C 255.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.81;MQ0=2;QD=21.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,10:12:27:284,27,0
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|
3301 chr1 129983 . C T 208.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.67;MQ0=2;QD=18.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,9:11:24:237,24,0
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|
3302 chr1 129984 . T C 217.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.67;MQ0=2;QD=19.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,9:11:24:246,24,0
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|
3303 chr1 130090 . A G 197.8 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.000;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=4.6635;MLEAC=2;MLEAF=1.00;MQ=23.48;MQ0=0;MQRankSum=0.290;QD=16.48;ReadPosRankSum=-1.448;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:1,11:12:21:226,21,0
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3304 chr1 130092 . A G 197.8 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.752;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=4.6635;MLEAC=2;MLEAF=1.00;MQ=23.48;MQ0=0;MQRankSum=0.752;QD=16.48;ReadPosRankSum=-0.752;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,10:12:21:226,21,0
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3305 chr1 130105 . T G 496.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.063;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=1.6988;MLEAC=2;MLEAF=1.00;MQ=30.50;MQ0=1;MQRankSum=1.449;QD=23.66;ReadPosRankSum=-1.701;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:3,18:21:45:525,45,0
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3306 chr1 130186 . G A 309.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.10;MQ0=2;QD=25.81;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,10:12:30:338,30,0
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3307 chr1 130188 . G A 307.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.10;MQ0=2;QD=25.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,10:12:30:336,30,0
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|
3308 chr1 130195 . G A 303.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.98;MQ0=0;QD=30.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:332,30,0
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3309 chr1 130203 . T C 188.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.02;MQ0=0;QD=26.97;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:217,21,0
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|
3310 chr1 130297 . C T 396.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.47;MQ0=0;QD=32.64;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:425,33,0
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3311 chr1 130299 . C T 391.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.47;MQ0=0;QD=32.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:420,33,0
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3312 chr1 130317 . G A 482.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.36;MQ0=0;QD=28.92;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:511,39,0
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3313 chr1 130321 . G A 485.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.36;MQ0=0;QD=31.64;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:514,39,0
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3314 chr1 130322 . G A 476.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.36;MQ0=0;QD=31.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:505,39,0
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3315 chr1 130326 . A G 488.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.36;MQ0=0;QD=27.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:517,39,0
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3316 chr1 130345 . T C 618.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.48;MQ0=0;QD=32.54;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:647,48,0
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3317 chr1 130362 . C T 595.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.33;MQ0=0;QD=29.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:624,48,0
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3318 chr1 130369 . A G 530.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.78;MQ0=0;QD=34.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:559,42,0
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3319 chr1 130374 . T C 645.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.35;MQ0=0;QD=31.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:674,51,0
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3320 chr1 130382 . T C 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.395;DP=19;Dels=0.00;FS=9.745;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.14;MQ0=0;MQRankSum=-1.395;QD=20.51;ReadPosRankSum=1.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:7,12:19:99:418,0,230
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3321 chr1 130392 . G A 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.223;DP=16;Dels=0.00;FS=10.532;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=0;MQRankSum=-1.059;QD=17.24;ReadPosRankSum=1.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:7,9:16:99:304,0,242
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3322 chr1 130395 . G A 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.107;DP=17;Dels=0.00;FS=10.843;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.81;MQ0=0;MQRankSum=-1.107;QD=16.63;ReadPosRankSum=1.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:8,9:17:99:311,0,277
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3323 chr1 130406 . G A 733.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.63;MQ0=0;QD=33.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:762,57,0
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3324 chr1 130422 . G A 680.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.44;MQ0=0;QD=27.30;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,19:19:54:709,54,0
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3325 chr1 130428 . C T 234.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=20;Dels=0.00;FS=13.778;HaplotypeScore=21.2632;MLEAC=1;MLEAF=0.500;MQ=55.68;MQ0=0;MQRankSum=0.501;QD=11.74;ReadPosRankSum=1.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:12,8:20:99:263,0,382
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3326 chr1 130463 . T A 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.131;DP=33;Dels=0.00;FS=33.092;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=0;MQRankSum=1.767;QD=13.30;ReadPosRankSum=0.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:467,0,604
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3327 chr1 130464 . T A 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.665;DP=34;Dels=0.00;FS=25.025;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=-1.006;QD=16.52;ReadPosRankSum=-0.104;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:15,19:34:99:590,0,499
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|
3328 chr1 130471 . G T 498.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.398;DP=36;Dels=0.00;FS=24.517;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=0.430;QD=13.85;ReadPosRankSum=0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:527,0,659
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|
3329 chr1 130515 . C T 710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.442;DP=43;Dels=0.00;FS=6.930;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-0.717;QD=16.53;ReadPosRankSum=-0.255;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:739,0,723
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|
|
3330 chr1 130542 . C T 93.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.025;DP=53;Dels=0.00;FS=1.790;HaplotypeScore=19.9950;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.161;QD=1.77;ReadPosRankSum=-3.267;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:45,8:53:99:122,0,1658
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|
3331 chr1 130586 . C T 933.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.100;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.060;QD=18.68;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:19,31:50:99:962,0,598
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|
3332 chr1 130630 . G A 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.871;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=19.8889;MLEAC=1;MLEAF=0.500;MQ=58.60;MQ0=0;MQRankSum=0.154;QD=17.07;ReadPosRankSum=-0.666;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:745,0,563
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|
|
3333 chr1 130682 . A C 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.424;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=-0.407;QD=11.69;ReadPosRankSum=-0.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:34,21:55:99:671,0,1176
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|
|
3334 chr1 130699 . G A 1434.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.474;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=0.851;QD=23.14;ReadPosRankSum=-0.956;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,42:62:99:1463,0,623
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|
|
3335 chr1 130768 . C T 1247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.238;DP=53;Dels=0.00;FS=14.260;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.41;MQ0=0;MQRankSum=0.829;QD=23.54;ReadPosRankSum=-1.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,36:53:99:1276,0,522
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|
|
3336 chr1 130839 . A G 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.077;DP=36;Dels=0.00;FS=2.873;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.222;QD=17.69;ReadPosRankSum=1.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,19:36:99:665,0,568
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|
|
3337 chr1 130852 . C G 1575.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.648;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=0.127;QD=22.42;ReadPosRankSum=0.887;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:1,40:41:99:1604,120,0
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|
|
3338 chr1 130914 . A G 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.017;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.258;QD=22.52;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:16,32:48:99:1109,0,452
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|
|
3339 chr1 130927 . A C 1100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.739;DP=48;Dels=0.00;FS=6.248;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.498;QD=22.93;ReadPosRankSum=2.329;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:16,32:48:99:1129,0,467
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|
|
3340 chr1 130951 . A G 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.242;DP=43;Dels=0.00;FS=7.186;HaplotypeScore=26.1290;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-1.231;QD=23.90;ReadPosRankSum=1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:14,29:43:99:1056,0,426
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|
|
3341 chr1 130966 . A T 1310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.444;DP=53;Dels=0.00;FS=6.248;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.819;QD=24.73;ReadPosRankSum=-1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,38:53:99:1339,0,440
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|
|
3342 chr1 130976 . G C 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.645;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=-0.337;QD=9.57;ReadPosRankSum=1.048;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:34,18:52:99:526,0,1151
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|
|
3343 chr1 130992 . C T 1237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.042;DP=57;Dels=0.00;FS=3.924;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=1.112;QD=21.72;ReadPosRankSum=-1.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:20,37:57:99:1266,0,611
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|
|
3344 chr1 131017 . C G 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.370;DP=49;Dels=0.00;FS=19.446;HaplotypeScore=1.9986;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=0.850;QD=16.36;ReadPosRankSum=1.350;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:830,0,803
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|
|
3345 chr1 131080 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=39;Dels=0.00;FS=1.261;HaplotypeScore=9.7317;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=0;MQRankSum=-0.662;QD=13.66;ReadPosRankSum=-0.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:561,0,711
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|
|
3346 chr1 131092 . A T 804.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.419;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=29.6879;MLEAC=1;MLEAF=0.500;MQ=54.75;MQ0=0;MQRankSum=2.039;QD=20.12;ReadPosRankSum=0.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,25:40:99:833,0,436
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|
|
3347 chr1 131093 . A T 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.421;DP=40;Dels=0.00;FS=5.618;HaplotypeScore=29.6879;MLEAC=1;MLEAF=0.500;MQ=54.75;MQ0=0;MQRankSum=-0.234;QD=5.22;ReadPosRankSum=1.390;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:30,10:40:99:237,0,1057
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|
3348 chr1 131106 . A G 434.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.361;DP=32;Dels=0.00;FS=8.080;HaplotypeScore=2.9994;MLEAC=1;MLEAF=0.500;MQ=52.01;MQ0=0;MQRankSum=-2.945;QD=13.59;ReadPosRankSum=-0.944;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:17,15:32:99:463,0,546
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|
|
3349 chr1 131121 . C T 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.467;DP=34;Dels=0.00;FS=5.188;HaplotypeScore=15.7761;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=-3.640;QD=15.90;ReadPosRankSum=-2.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:569,0,510
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|
|
3350 chr1 131126 . C A 1433.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=15.7761;MLEAC=2;MLEAF=1.00;MQ=53.11;MQ0=0;QD=32.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1462,111,0
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3351 chr1 131132 . C A 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.426;DP=44;Dels=0.00;FS=15.097;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=53.78;MQ0=0;MQRankSum=4.844;QD=17.24;ReadPosRankSum=-1.049;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:787,0,609
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3352 chr1 131154 . A T 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;DP=44;Dels=0.00;FS=23.397;HaplotypeScore=4.4675;MLEAC=1;MLEAF=0.500;MQ=52.56;MQ0=0;MQRankSum=-4.184;QD=14.54;ReadPosRankSum=2.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:668,0,759
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3353 chr1 131158 . C T 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.954;DP=41;Dels=0.00;FS=21.509;HaplotypeScore=4.4675;MLEAC=1;MLEAF=0.500;MQ=52.27;MQ0=0;MQRankSum=-3.830;QD=13.41;ReadPosRankSum=2.131;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:578,0,692
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|
3354 chr1 131163 . T C 1650.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=3.4677;MLEAC=2;MLEAF=1.00;MQ=51.91;MQ0=0;QD=32.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1679,129,0
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|
|
3355 chr1 131170 . T G 560.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.488;DP=49;Dels=0.00;FS=38.825;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=51.91;MQ0=0;MQRankSum=-3.211;QD=11.44;ReadPosRankSum=1.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:589,0,938
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|
3356 chr1 131184 . G A 432.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.436;DP=49;Dels=0.00;FS=38.784;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.16;MQ0=2;MQRankSum=-3.020;QD=8.83;ReadPosRankSum=-0.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:33,16:49:99:461,0,1001
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3357 chr1 131207 . G T 418.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.185;DP=42;Dels=0.00;FS=27.416;HaplotypeScore=4.4038;MLEAC=1;MLEAF=0.500;MQ=48.07;MQ0=2;MQRankSum=-3.576;QD=9.97;ReadPosRankSum=-4.554;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:447,0,821
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|
|
3358 chr1 131225 . C G 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.578;DP=40;Dels=0.00;FS=16.577;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.44;MQ0=3;MQRankSum=-2.808;QD=6.19;ReadPosRankSum=-0.548;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:29,11:40:99:276,0,822
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|
|
3359 chr1 131249 . C T 126.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.731;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.12;MQ0=0;MQRankSum=0.731;QD=25.21;ReadPosRankSum=-0.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:1,4:5:12:154,12,0
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|
3360 chr1 131267 . T A 654.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.56;MQ0=1;QD=34.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,19:19:51:683,51,0
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|
3361 chr1 131275 . T C 693.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.79;MQ0=1;QD=34.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,20:20:54:722,54,0
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|
|
3362 chr1 131301 . T C 198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.737;DP=31;Dels=0.00;FS=14.239;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=57.02;MQ0=3;MQRankSum=0.331;QD=6.41;ReadPosRankSum=-2.212;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:21,10:31:99:227,0,719
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|
|
3363 chr1 131355 . A G 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.377;DP=32;Dels=0.00;FS=6.200;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=1;MQRankSum=0.099;QD=15.24;ReadPosRankSum=0.298;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:14,18:32:99:516,0,481
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|
|
3364 chr1 131363 . A C 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.895;DP=30;Dels=0.00;FS=4.091;HaplotypeScore=8.8267;MLEAC=1;MLEAF=0.500;MQ=57.13;MQ0=1;MQRankSum=-1.768;QD=15.03;ReadPosRankSum=1.200;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:14,16:30:99:479,0,438
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|
|
3365 chr1 131370 . T C 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.262;DP=35;Dels=0.00;FS=6.017;HaplotypeScore=8.8267;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=1;MQRankSum=2.012;QD=12.54;ReadPosRankSum=0.262;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:21,14:35:99:467,0,650
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|
|
3366 chr1 131393 . T A 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.277;DP=35;Dels=0.00;FS=2.127;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=1;MQRankSum=-1.006;QD=16.68;ReadPosRankSum=0.486;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:612,0,506
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|
|
3367 chr1 131394 . T G 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.035;DP=35;Dels=0.00;FS=2.127;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=1;MQRankSum=-2.497;QD=16.71;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:613,0,502
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|
|
3368 chr1 131430 . C G 1471.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.04;MQ0=1;QD=27.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1500,117,0
|
|
|
3369 chr1 131432 . G C 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.327;DP=42;Dels=0.00;FS=5.360;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=1;MQRankSum=-1.274;QD=17.66;ReadPosRankSum=1.668;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:18,24:42:99:770,0,563
|
|
|
3370 chr1 131475 . G T 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.053;DP=48;Dels=0.00;FS=2.505;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.99;MQ0=1;MQRankSum=0.096;QD=15.00;ReadPosRankSum=0.947;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:748,0,812
|
|
|
3371 chr1 131486 . C G 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.407;DP=50;Dels=0.00;FS=2.434;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=60.59;MQ0=0;MQRankSum=0.601;QD=16.58;ReadPosRankSum=-1.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:857,0,830
|
|
|
3372 chr1 131560 . C T 2155.77 . AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=30.7936;MLEAC=2;MLEAF=1.00;MQ=54.35;MQ0=0;QD=30.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,58:58:99:2184,169,0
|
|
|
3373 chr1 131561 . A G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.975;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=33.7934;MLEAC=1;MLEAF=0.500;MQ=52.54;MQ0=0;MQRankSum=4.289;QD=12.63;ReadPosRankSum=2.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,25:63:99:824,0,1054
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|
|
3374 chr1 131579 . T A 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.134;DP=55;Dels=0.00;FS=1.050;HaplotypeScore=2.6642;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=3.452;QD=14.49;ReadPosRankSum=-1.717;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,25:55:99:825,0,902
|
|
|
3375 chr1 131583 . G A 2053.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=2.6642;MLEAC=2;MLEAF=1.00;MQ=51.43;MQ0=0;QD=27.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2082,162,0
|
|
|
3376 chr1 131601 . G A 779.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.21;MQ0=0;QD=26.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:808,63,0
|
|
|
3377 chr1 131602 . T C 819.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.21;MQ0=0;QD=28.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:848,63,0
|
|
|
3378 chr1 131633 . G T 907.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.40;MQ0=0;QD=28.45;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:936,69,0
|
|
|
3379 chr1 131703 . T C 2110.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=56.70;MQ0=1;QD=34.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,54:55:99:2139,160,0
|
|
|
3380 chr1 131720 . T C 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.158;DP=55;Dels=0.00;FS=3.715;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=-1.715;QD=13.65;ReadPosRankSum=4.883;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,25:55:99:779,0,1056
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|
|
3381 chr1 131746 . G A 1546.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=2;QD=31.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:1,42:43:99:1575,120,0
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|
|
3382 chr1 131760 . C T 612.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.593;DP=39;Dels=0.00;FS=7.125;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.06;MQ0=2;MQRankSum=1.717;QD=15.71;ReadPosRankSum=0.927;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:641,0,573
|
|
|
3383 chr1 131770 . G A,C 1088.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.27;MQ0=3;QD=28.64;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/2:2,18,18:38:99:1278,681,630,597,0,543
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|
|
3384 chr1 131775 . T C 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.080;DP=35;Dels=0.00;FS=5.188;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.37;MQ0=2;MQRankSum=-1.927;QD=13.85;ReadPosRankSum=-1.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:513,0,603
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|
|
3385 chr1 131776 . G A 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.441;DP=33;Dels=0.00;FS=3.192;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.73;MQ0=2;MQRankSum=-2.203;QD=12.42;ReadPosRankSum=-0.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:438,0,599
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|
|
3386 chr1 131796 . A G 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.532;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.71;MQ0=2;MQRankSum=-2.445;QD=10.05;ReadPosRankSum=0.780;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,14:36:99:390,0,704
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|
|
3387 chr1 131801 . A G 678.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.366;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.91;MQ0=2;MQRankSum=2.114;QD=19.39;ReadPosRankSum=-1.067;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,21:35:99:707,0,371
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|
|
3388 chr1 131805 . G C 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.002;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.83;MQ0=2;MQRankSum=2.434;QD=19.64;ReadPosRankSum=-1.129;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,24:39:99:794,0,392
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|
|
3389 chr1 131806 . A G 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.239;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.83;MQ0=2;MQRankSum=-2.752;QD=9.10;ReadPosRankSum=1.129;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:383,0,799
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|
|
3390 chr1 131818 . T C 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.568;DP=39;Dels=0.00;FS=1.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.16;MQ0=2;MQRankSum=-2.677;QD=7.05;ReadPosRankSum=0.600;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:303,0,803
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|
|
3391 chr1 131851 . A G 306.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.046;DP=41;Dels=0.00;FS=5.599;HaplotypeScore=20.1968;MLEAC=1;MLEAF=0.500;MQ=52.36;MQ0=1;MQRankSum=-3.302;QD=7.48;ReadPosRankSum=-1.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,12:41:99:335,0,851
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|
|
3392 chr1 131940 . C T 523.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.576;DP=33;Dels=0.00;FS=13.038;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.25;MQ0=1;MQRankSum=0.537;QD=15.87;ReadPosRankSum=-0.230;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:13,20:33:99:552,0,366
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|
|
3393 chr1 131946 . T G 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.071;DP=33;Dels=0.00;FS=13.019;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.15;MQ0=1;MQRankSum=-0.754;QD=7.81;ReadPosRankSum=-0.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,11:33:99:286,0,622
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|
|
3394 chr1 131950 . G A 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.061;DP=33;Dels=0.00;FS=9.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.67;MQ0=1;MQRankSum=-0.793;QD=6.69;ReadPosRankSum=-0.468;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,10:33:99:249,0,652
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|
|
3395 chr1 131964 . T C 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.757;DP=27;Dels=0.00;FS=4.809;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.64;MQ0=1;MQRankSum=-0.976;QD=1.70;ReadPosRankSum=-2.017;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,5:27:74:74,0,639
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|
|
3396 chr1 131985 . A T 612.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.63;MQ0=1;QD=29.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,21:21:51:641,51,0
|
|
|
3397 chr1 132042 . C T 418.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.17;MQ0=4;QD=19.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,21:21:36:447,36,0
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|
|
3398 chr1 132048 . T A 299.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.822;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.89;MQ0=4;MQRankSum=1.734;QD=16.65;ReadPosRankSum=1.187;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:6,12:18:27:328,27,0
|
|
|
3399 chr1 132089 . A T 110.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.747;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=3.9529;MLEAC=2;MLEAF=1.00;MQ=18.63;MQ0=4;MQRankSum=0.747;QD=9.17;ReadPosRankSum=-0.747;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:1,11:12:12:138,12,0
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|
|
3400 chr1 132209 . C T 107.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=2.8995;MLEAC=2;MLEAF=1.00;MQ=34.81;MQ0=0;QD=26.76;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:135,12,0
|
|
|
3401 chr1 132286 . C T 954.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.87;MQ0=1;QD=29.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,32:32:78:983,78,0
|
|
|
3402 chr1 132307 . T C 759.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.61;MQ0=0;QD=29.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,25:26:63:788,63,0
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|
|
3403 chr1 132327 . A T 140.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.844;DP=18;Dels=0.00;FS=4.832;HaplotypeScore=1.9663;MLEAC=1;MLEAF=0.500;MQ=44.38;MQ0=0;MQRankSum=-2.266;QD=7.82;ReadPosRankSum=1.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:10,8:18:99:169,0,314
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|
|
3404 chr1 132328 . A T 140.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.755;DP=18;Dels=0.00;FS=4.832;HaplotypeScore=1.9663;MLEAC=1;MLEAF=0.500;MQ=44.38;MQ0=0;MQRankSum=-2.532;QD=7.82;ReadPosRankSum=1.644;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:10,8:18:99:169,0,315
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|
|
3405 chr1 132332 . A T 137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.400;DP=18;Dels=0.00;FS=4.832;HaplotypeScore=1.9663;MLEAC=1;MLEAF=0.500;MQ=44.38;MQ0=0;MQRankSum=-2.355;QD=7.65;ReadPosRankSum=1.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:10,8:18:99:166,0,314
|
|
|
3406 chr1 132348 . G A 209.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.371;DP=24;Dels=0.00;FS=4.738;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=46.07;MQ0=0;MQRankSum=1.431;QD=8.74;ReadPosRankSum=1.789;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:15,9:24:99:238,0,433
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|
|
3407 chr1 132356 . A C 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.968;DP=24;Dels=0.00;FS=4.738;HaplotypeScore=14.3879;MLEAC=1;MLEAF=0.500;MQ=45.87;MQ0=0;MQRankSum=-2.087;QD=16.82;ReadPosRankSum=-0.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:9,15:24:99:432,0,228
|
|
|
3408 chr1 132369 . A T 44.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.273;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.53;MQ0=0;MQRankSum=-0.634;QD=1.95;ReadPosRankSum=1.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,5:23:73:73,0,558
|
|
|
3409 chr1 132372 . A T 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.501;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.51;MQ0=0;MQRankSum=-0.203;QD=0.52;ReadPosRankSum=2.068;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,4:23:40:40,0,597
|
|
|
3410 chr1 132376 . T A 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.014;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.51;MQ0=0;MQRankSum=-0.203;QD=0.56;ReadPosRankSum=1.419;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,4:23:41:41,0,600
|
|
|
3411 chr1 132383 . A C 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.276;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.49;MQ0=0;MQRankSum=-0.142;QD=0.75;ReadPosRankSum=-0.614;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:16,4:20:43:43,0,566
|
|
|
3412 chr1 132405 . G A 755.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.18;MQ0=2;QD=32.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,23:23:60:784,60,0
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|
|
3413 chr1 132443 . C T 984.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.73;MQ0=2;QD=29.79;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1013,78,0
|
|
|
3414 chr1 132456 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.241;DP=28;Dels=0.00;FS=1.941;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=50.78;MQ0=2;MQRankSum=0.212;QD=22.35;ReadPosRankSum=0.393;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:9,18:28:99:654,0,184
|
|
|
3415 chr1 132468 . C G 1263.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.51;MQ0=2;QD=32.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1292,99,0
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|
|
3416 chr1 132478 . T C 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.382;DP=36;Dels=0.00;FS=3.155;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.69;MQ0=2;MQRankSum=0.673;QD=9.83;ReadPosRankSum=-0.071;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:382,0,743
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|
|
3417 chr1 132621 . A G 898.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.333;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=1.9970;MLEAC=2;MLEAF=1.00;MQ=54.48;MQ0=0;MQRankSum=-0.800;QD=34.57;ReadPosRankSum=1.600;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:1,25:26:42:927,42,0
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|
|
3418 chr1 132697 . G T 1425.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.63;MQ0=1;QD=28.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1454,108,0
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|
|
3419 chr1 132730 . G C 244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.108;DP=40;Dels=0.00;FS=1.399;HaplotypeScore=2.7317;MLEAC=1;MLEAF=0.500;MQ=52.84;MQ0=1;MQRankSum=-4.323;QD=6.12;ReadPosRankSum=-0.421;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,11:40:99:273,0,1019
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|
|
3420 chr1 132737 . C T 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.263;DP=48;Dels=0.00;FS=1.273;HaplotypeScore=23.7282;MLEAC=1;MLEAF=0.500;MQ=51.85;MQ0=2;MQRankSum=-4.842;QD=7.04;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,14:48:99:366,0,1103
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|
|
3421 chr1 132780 . A G 358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.056;DP=55;Dels=0.00;FS=28.806;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.41;MQ0=1;MQRankSum=2.043;QD=6.52;ReadPosRankSum=-0.819;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,15:55:99:387,0,1434
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|
|
3422 chr1 132838 . G A 841.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.471;DP=60;Dels=0.00;FS=19.671;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.32;MQ0=0;MQRankSum=-0.669;QD=14.03;ReadPosRankSum=1.055;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,27:60:99:870,0,1128
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|
|
3423 chr1 132869 . G T 2120.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.59;MQ0=0;QD=30.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2149,166,0
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|
|
3424 chr1 132921 . T C 1226.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=47.64;MQ0=0;QD=32.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1255,96,0
|
|
|
3425 chr1 132922 . T C 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.083;DP=32;Dels=0.00;FS=15.134;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=47.64;MQ0=0;MQRankSum=-1.652;QD=17.87;ReadPosRankSum=1.500;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,18:32:99:600,0,462
|
|
|
3426 chr1 132923 . G T 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.083;DP=32;Dels=0.00;FS=15.134;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=47.64;MQ0=0;MQRankSum=-1.842;QD=17.65;ReadPosRankSum=1.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,18:32:99:593,0,451
|
|
|
3427 chr1 132956 . T C 1509.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=64.3730;MLEAC=2;MLEAF=1.00;MQ=53.28;MQ0=0;QD=28.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1538,117,0
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|
|
3428 chr1 133042 . G A 1488.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.72;MQ0=0;QD=34.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1517,120,0
|
|
|
3429 chr1 133059 . C T 705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.463;DP=46;Dels=0.00;FS=11.451;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.52;MQ0=0;MQRankSum=-2.139;QD=15.34;ReadPosRankSum=-0.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:734,0,651
|
|
|
3430 chr1 133068 . T C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.081;DP=44;Dels=0.00;FS=11.681;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=48.47;MQ0=0;MQRankSum=-2.420;QD=14.97;ReadPosRankSum=-0.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:687,0,652
|
|
|
3431 chr1 133104 . T C 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.990;DP=47;Dels=0.00;FS=4.125;HaplotypeScore=2.9633;MLEAC=1;MLEAF=0.500;MQ=52.43;MQ0=0;MQRankSum=1.309;QD=14.85;ReadPosRankSum=-0.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:726,0,732
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|
|
3432 chr1 133115 . C G 712.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.406;DP=46;Dels=0.00;FS=2.550;HaplotypeScore=2.9394;MLEAC=1;MLEAF=0.500;MQ=52.55;MQ0=0;MQRankSum=-1.164;QD=15.49;ReadPosRankSum=0.505;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:741,0,689
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|
|
3433 chr1 133160 . A T 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=24.1627;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=2.042;QD=14.09;ReadPosRankSum=0.744;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:592,0,613
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|
|
3434 chr1 133168 . T A 1301.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=72.4881;MLEAC=2;MLEAF=1.00;MQ=50.41;MQ0=0;QD=30.97;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1330,105,0
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|
|
3435 chr1 133318 . T G 1696.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=56.63;MQ0=0;QD=27.68;EFF=UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1725,132,0
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|
|
3436 chr1 133344 . T C 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.470;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=0.230;QD=15.59;ReadPosRankSum=0.150;EFF=UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:792,0,735
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|
3437 chr1 133348 . G T 1903.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.70;MQ0=0;QD=33.82;EFF=UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1932,150,0
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|
|
3438 chr1 133404 . G T 940.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.824;DP=49;Dels=0.00;FS=1.131;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=3.143;QD=19.20;ReadPosRankSum=0.559;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:20,29:49:99:969,0,589
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|
|
3439 chr1 133419 . G C 1742.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.29;MQ0=0;QD=33.58;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1771,138,0
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|
|
3440 chr1 133433 . G A 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.624;DP=39;Dels=0.00;FS=1.390;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=0;MQRankSum=-4.245;QD=8.51;ReadPosRankSum=0.593;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:27,12:39:99:360,0,943
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|
|
3441 chr1 133435 . A T 1273.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.45;MQ0=0;QD=26.76;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1302,102,0
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|
|
3442 chr1 133436 . A T 1250.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.45;MQ0=0;QD=27.76;EFF=START_GAINED(LOW||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1279,99,0
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|
|
3443 chr1 133437 . G C 1319.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.45;MQ0=0;QD=27.96;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1348,102,0
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|
|
3444 chr1 133448 . C A 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.362;DP=47;Dels=0.00;FS=1.146;HaplotypeScore=1.5317;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-4.461;QD=10.08;ReadPosRankSum=-0.365;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:30,17:47:99:502,0,1052
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|
|
3445 chr1 133453 . C T 520.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.012;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=16.0294;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=0;MQRankSum=-4.142;QD=10.85;ReadPosRankSum=-0.245;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:30,18:48:99:549,0,976
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|
|
3446 chr1 133491 . T A,G 1599.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=57.45;MQ0=0;QD=30.76;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 1/2:0,20,32:52:99:1838,1129,1068,710,0,616
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|
3447 chr1 133511 . T G 1608.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=57.68;MQ0=0;QD=27.83;EFF=START_GAINED(LOW||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1637,126,0
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3448 chr1 133553 . A G 417.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.865;DP=46;Dels=0.00;FS=8.994;HaplotypeScore=2.6278;MLEAC=1;MLEAF=0.500;MQ=56.55;MQ0=0;MQRankSum=-4.347;QD=9.08;ReadPosRankSum=0.657;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:30,16:46:99:446,0,1041
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3449 chr1 133580 . G T 655.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=46;Dels=0.00;FS=8.283;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.24;MQ0=0;MQRankSum=-5.226;QD=14.26;ReadPosRankSum=-1.808;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:25,21:46:99:684,0,798
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3450 chr1 133584 . G A 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.057;DP=45;Dels=0.00;FS=4.288;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-5.037;QD=13.24;ReadPosRankSum=-1.450;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:25,20:45:99:624,0,830
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|
3451 chr1 133629 . G A 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.488;DP=53;Dels=0.00;FS=2.379;HaplotypeScore=3.9941;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=-5.817;QD=14.45;ReadPosRankSum=0.793;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:28,25:53:99:794,0,922
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|
3452 chr1 133703 . G A 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.177;DP=47;Dels=0.00;FS=1.150;HaplotypeScore=11.4011;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=-5.657;QD=8.59;ReadPosRankSum=0.492;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:29,18:47:99:432,0,1026
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|
3453 chr1 133708 . C T 327.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.987;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=11.4011;MLEAC=1;MLEAF=0.500;MQ=54.07;MQ0=0;MQRankSum=-4.162;QD=6.83;ReadPosRankSum=-1.463;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:34,14:48:99:356,0,1139
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|
3454 chr1 133768 . C T 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.666;DP=35;Dels=0.00;FS=3.120;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.03;MQ0=0;MQRankSum=-3.499;QD=9.74;ReadPosRankSum=0.802;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:22,13:35:99:369,0,766
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|
|
3455 chr1 133772 . T A 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.647;DP=31;Dels=0.00;FS=1.503;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=0;MQRankSum=-2.798;QD=11.86;ReadPosRankSum=-0.258;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:17,14:31:99:396,0,591
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|
|
3456 chr1 133877 . G C 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.348;DP=64;Dels=0.00;FS=2.113;HaplotypeScore=9.9811;MLEAC=1;MLEAF=0.500;MQ=48.82;MQ0=0;MQRankSum=-3.336;QD=12.97;ReadPosRankSum=1.698;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V19|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,28:64:99:858,0,1194
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|
|
3457 chr1 133880 . T G 161.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.904;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=9.9811;MLEAC=1;MLEAF=0.500;MQ=48.53;MQ0=0;MQRankSum=-1.770;QD=2.61;ReadPosRankSum=2.191;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcG|S20|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:52,10:62:99:190,0,1843
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|
|
3458 chr1 133924 . C T 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.234;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=14.4642;MLEAC=1;MLEAF=0.500;MQ=50.02;MQ0=1;MQRankSum=-2.145;QD=5.48;ReadPosRankSum=0.419;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P35L|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:38,12:50:99:302,0,1267
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|
|
3459 chr1 133955 . C G 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.925;DP=31;Dels=0.00;FS=1.768;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=49.62;MQ0=0;MQRankSum=-2.415;QD=5.06;ReadPosRankSum=-1.377;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D45E|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,8:31:99:185,0,789
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|
|
3460 chr1 133985 . C T 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.181;DP=21;Dels=0.00;FS=15.849;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.52;MQ0=1;MQRankSum=-2.976;QD=1.42;ReadPosRankSum=-2.032;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C55|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:16,5:21:58:58,0,571
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|
|
3461 chr1 134007 . G T 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.146;DP=26;Dels=0.00;FS=3.862;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.17;MQ0=1;MQRankSum=-3.466;QD=6.64;ReadPosRankSum=-0.903;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V63L|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:17,9:26:99:201,0,596
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|
|
3462 chr1 134011 . C T 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.206;DP=30;Dels=0.00;FS=3.630;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.39;MQ0=1;MQRankSum=-3.372;QD=7.46;ReadPosRankSum=-0.619;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A64V|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,11:30:99:252,0,660
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|
|
3463 chr1 134033 . A G 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.577;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=39.69;MQ0=2;MQRankSum=-1.710;QD=0.33;ReadPosRankSum=-2.732;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L71|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,6:39:41:41,0,1056
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|
|
3464 chr1 134148 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.729;DP=60;Dels=0.00;FS=15.632;HaplotypeScore=2.9570;MLEAC=1;MLEAF=0.500;MQ=39.89;MQ0=8;MQRankSum=1.349;QD=8.15;ReadPosRankSum=0.912;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R110C|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:41,19:60:99:517,0,973
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|
|
3465 chr1 134280 . A C 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.793;DP=91;Dels=0.00;FS=2.074;HaplotypeScore=10.4073;MLEAC=1;MLEAF=0.500;MQ=34.28;MQ0=7;MQRankSum=1.802;QD=10.80;ReadPosRankSum=-0.414;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K154Q|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,38:91:99:1011,0,1041
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|
|
3466 chr1 134333 . T C 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.529;DP=65;Dels=0.00;FS=5.430;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.88;MQ0=7;MQRankSum=0.576;QD=10.38;ReadPosRankSum=0.734;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y171|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:41,24:65:99:703,0,1008
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|
|
3467 chr1 134354 . T C 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.370;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.63;MQ0=7;MQRankSum=0.036;QD=9.56;ReadPosRankSum=-0.060;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A178|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,21:51:99:516,0,788
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|
|
3468 chr1 134514 . T C 363.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.334;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.7876;MLEAC=1;MLEAF=0.500;MQ=37.13;MQ0=3;MQRankSum=-2.851;QD=7.28;ReadPosRankSum=-0.527;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C232R|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:392,0,878
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|
|
3469 chr1 134570 . T C 854.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.545;DP=44;Dels=0.00;FS=1.192;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.49;MQ0=0;MQRankSum=3.436;QD=19.43;ReadPosRankSum=-1.090;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F250|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:883,0,419
|
|
|
3470 chr1 134580 . C T 1494.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.09;MQ0=0;QD=33.97;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P254S|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1523,117,0
|
|
|
3471 chr1 134603 . G T 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.394;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.9762;MLEAC=1;MLEAF=0.500;MQ=42.98;MQ0=0;MQRankSum=-4.437;QD=12.42;ReadPosRankSum=-1.075;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acT|T261|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:612,0,769
|
|
|
3472 chr1 134696 . G A 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.174;DP=25;Dels=0.00;FS=7.471;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=32.51;MQ0=1;MQRankSum=1.217;QD=13.63;ReadPosRankSum=-3.187;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R292|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:11,14:25:99:369,0,240
|
|
|
3473 chr1 134729 . G T 259.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.888;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=3.8313;MLEAC=2;MLEAF=1.00;MQ=20.10;MQ0=6;MQRankSum=1.678;QD=13.67;ReadPosRankSum=1.283;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G303|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:2,17:19:30:288,30,0
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|
|
3474 chr1 134730 . T G 147.89 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.715;DP=17;Dels=0.00;FS=9.031;HaplotypeScore=3.8313;MLEAC=1;MLEAF=0.500;MQ=18.34;MQ0=6;MQRankSum=0.715;QD=8.70;ReadPosRankSum=1.931;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Gtc|F304V|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:3,14:17:2:174,0,2
|
|
|
3475 chr1 134755 . G C 619.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.70;MQ0=7;QD=20.66;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aCt|S312T|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,30:30:54:648,54,0
|
|
|
3476 chr1 134780 . T C 422.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.579;DP=42;Dels=0.00;FS=7.420;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=32.71;MQ0=7;MQRankSum=0.050;QD=10.07;ReadPosRankSum=1.871;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C320|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:451,0,502
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|
|
3477 chr1 134807 . C T 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.282;DP=53;Dels=0.00;FS=2.402;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=34.74;MQ0=5;MQRankSum=-1.432;QD=14.07;ReadPosRankSum=0.010;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I329|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,33:53:99:774,0,584
|
|
|
3478 chr1 134822 . T C 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.627;DP=52;Dels=0.00;FS=4.058;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=36.11;MQ0=1;MQRankSum=-2.231;QD=16.55;ReadPosRankSum=0.789;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I334|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,33:52:99:889,0,575
|
|
|
3479 chr1 134927 . G C 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.760;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=5.3557;MLEAC=1;MLEAF=0.500;MQ=26.60;MQ0=9;MQRankSum=1.588;QD=7.44;ReadPosRankSum=-0.677;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E369D|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,19:52:99:415,0,456
|
|
|
3480 chr1 135009 . A G 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.634;DP=56;Dels=0.00;FS=9.949;HaplotypeScore=1.8154;MLEAC=1;MLEAF=0.500;MQ=45.81;MQ0=1;MQRankSum=-2.335;QD=0.23;ReadPosRankSum=-2.281;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T397A|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,6:56:41:41,0,1637
|
|
|
3481 chr1 135029 . G C 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.042;DP=68;Dels=0.00;FS=9.976;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=1;MQRankSum=-1.650;QD=2.79;ReadPosRankSum=-0.245;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttC|L403F|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:57,11:68:99:218,0,1758
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|
|
3482 chr1 135042 . A G 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.577;DP=75;Dels=0.00;FS=8.931;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=39.96;MQ0=1;MQRankSum=3.045;QD=8.50;ReadPosRankSum=0.420;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N408D|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,22:75:99:666,0,1347
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|
|
3483 chr1 135055 . A G 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.310;DP=84;Dels=0.00;FS=10.873;HaplotypeScore=9.3239;MLEAC=1;MLEAF=0.500;MQ=36.61;MQ0=3;MQRankSum=0.553;QD=3.71;ReadPosRankSum=1.854;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E412G|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:69,15:84:99:340,0,1652
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|
|
3484 chr1 135124 . A G 1965.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.982;DP=84;Dels=0.00;FS=3.513;HaplotypeScore=1.9965;MLEAC=1;MLEAF=0.500;MQ=34.13;MQ0=5;MQRankSum=2.897;QD=23.40;ReadPosRankSum=0.921;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q435R|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:16,68:84:99:1994,0,139
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|
|
3485 chr1 135152 . T C 107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.499;DP=86;Dels=0.00;FS=1.215;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.34;MQ0=3;MQRankSum=-0.614;QD=1.25;ReadPosRankSum=0.942;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D444|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,14:86:99:136,0,2271
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|
|
3486 chr1 135153 . G A 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.997;DP=87;Dels=0.00;FS=1.186;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=37.69;MQ0=3;MQRankSum=-0.409;QD=1.65;ReadPosRankSum=0.537;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V445M|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,15:87:99:172,0,2269
|
|
|
3487 chr1 135160 . C G 200.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.067;DP=80;Dels=0.00;FS=2.719;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=38.64;MQ0=3;MQRankSum=0.297;QD=2.51;ReadPosRankSum=1.116;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S447C|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:66,14:80:99:229,0,2067
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|
|
3488 chr1 135180 . T A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.230;DP=74;Dels=0.00;FS=21.668;HaplotypeScore=16.1489;MLEAC=1;MLEAF=0.500;MQ=42.55;MQ0=0;MQRankSum=1.094;QD=3.70;ReadPosRankSum=1.690;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Att|F454I|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,13:74:99:302,0,1980
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|
|
3489 chr1 135182 . T C 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.302;DP=73;Dels=0.00;FS=22.648;HaplotypeScore=16.1489;MLEAC=1;MLEAF=0.500;MQ=42.76;MQ0=0;MQRankSum=-0.479;QD=10.89;ReadPosRankSum=1.077;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F454|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:44,29:73:99:823,0,1443
|
|
|
3490 chr1 135209 . A G 937.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.127;DP=78;Dels=0.00;FS=18.781;HaplotypeScore=10.8281;MLEAC=1;MLEAF=0.500;MQ=48.03;MQ0=0;MQRankSum=-2.484;QD=12.02;ReadPosRankSum=0.229;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A463|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:46,32:78:99:966,0,1557
|
|
|
3491 chr1 135218 . T C 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.068;DP=76;Dels=0.00;FS=7.732;HaplotypeScore=20.2693;MLEAC=1;MLEAF=0.500;MQ=49.54;MQ0=0;MQRankSum=-1.200;QD=6.59;ReadPosRankSum=-0.624;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S466|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:57,19:76:99:529,0,1942
|
|
|
3492 chr1 135220 . A G 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.987;DP=77;Dels=0.00;FS=5.434;HaplotypeScore=9.4397;MLEAC=1;MLEAF=0.500;MQ=49.95;MQ0=0;MQRankSum=-0.384;QD=6.30;ReadPosRankSum=-0.821;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E467G|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:58,19:77:99:513,0,1945
|
|
|
3493 chr1 135242 . G T 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.801;DP=84;Dels=0.00;FS=4.355;HaplotypeScore=23.7688;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=0;MQRankSum=-2.169;QD=10.69;ReadPosRankSum=-0.189;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P474|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:52,32:84:99:926,0,1735
|
|
|
3494 chr1 135249 . C A 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.078;DP=83;Dels=0.00;FS=0.951;HaplotypeScore=23.7688;MLEAC=1;MLEAF=0.500;MQ=53.90;MQ0=0;MQRankSum=3.080;QD=7.48;ReadPosRankSum=1.491;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Aca|P477T|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,22:83:99:649,0,2002
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|
|
3495 chr1 135260 . G C 1586.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.276;DP=77;Dels=0.00;FS=1.978;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.49;MQ0=0;MQRankSum=-0.838;QD=20.61;ReadPosRankSum=0.358;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A480|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,50:77:99:1615,0,861
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|
|
3496 chr1 135276 . C T 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.236;DP=78;Dels=0.00;FS=3.392;HaplotypeScore=25.9840;MLEAC=1;MLEAF=0.500;MQ=58.13;MQ0=0;MQRankSum=0.021;QD=9.15;ReadPosRankSum=0.503;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,25:78:99:742,0,1838
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|
|
3497 chr1 135284 . A G 909.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.412;DP=83;Dels=0.00;FS=0.867;HaplotypeScore=45.6804;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=2.555;QD=10.96;ReadPosRankSum=-0.735;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,30:83:99:938,0,1841
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|
|
3498 chr1 135290 . A G 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.543;DP=80;Dels=0.00;FS=3.316;HaplotypeScore=43.6813;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=-0.055;QD=11.50;ReadPosRankSum=-0.730;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,30:80:99:948,0,1404
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|
|
3499 chr1 135296 . T A 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.491;DP=77;Dels=0.00;FS=3.797;HaplotypeScore=25.7468;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.051;QD=7.83;ReadPosRankSum=0.366;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:55,22:77:99:631,0,2017
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|
|
3500 chr1 135305 . C A 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.358;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=18.7849;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-0.819;QD=2.55;ReadPosRankSum=-4.449;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:77,14:91:99:260,0,2802
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|
|
3501 chr1 135319 . A G 757.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.119;DP=101;Dels=0.00;FS=0.864;HaplotypeScore=3.9995;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.932;QD=7.50;ReadPosRankSum=-0.871;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:74,27:101:99:786,0,2632
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|
|
3502 chr1 135362 . G C 521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.995;DP=104;Dels=0.00;FS=0.933;HaplotypeScore=3.5999;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=-0.569;QD=5.02;ReadPosRankSum=1.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:82,21:104:99:550,0,2813
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|
|
3503 chr1 135376 . T C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.053;DP=104;Dels=0.00;FS=0.969;HaplotypeScore=2.8632;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-2.044;QD=4.12;ReadPosRankSum=0.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:85,19:104:99:457,0,2999
|
|
|
3504 chr1 135384 . G A 3914.77 . AC=2;AF=1.00;AN=2;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=22.8484;MLEAC=2;MLEAF=1.00;MQ=59.14;MQ0=0;QD=33.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,103:103:99:3943,301,0
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|
|
3505 chr1 135391 . T G 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.718;DP=103;Dels=0.00;FS=2.944;HaplotypeScore=27.2496;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=-0.169;QD=7.15;ReadPosRankSum=0.641;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:74,28:103:99:765,0,2417
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|
|
3506 chr1 135400 . G A 1703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.624;DP=108;Dels=0.00;FS=6.146;HaplotypeScore=26.0389;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-2.758;QD=15.78;ReadPosRankSum=-0.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:56,52:108:99:1732,0,1799
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|
|
3507 chr1 135425 . T C 2440.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=100;Dels=0.00;FS=5.702;HaplotypeScore=37.9722;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=-2.038;QD=24.41;ReadPosRankSum=-0.257;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,72:100:99:2469,0,843
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|
|
3508 chr1 135428 . G T 453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.762;DP=96;Dels=0.00;FS=3.339;HaplotypeScore=38.9718;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=-1.010;QD=4.73;ReadPosRankSum=0.124;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,21:96:99:482,0,2684
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|
|
3509 chr1 135433 . G T 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=100;Dels=0.00;FS=5.032;HaplotypeScore=76.9445;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=-4.688;QD=4.05;ReadPosRankSum=0.973;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:82,18:100:99:433,0,2862
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|
|
3510 chr1 135440 . A T 524.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.355;DP=97;Dels=0.00;FS=0.920;HaplotypeScore=61.9081;MLEAC=1;MLEAF=0.500;MQ=56.90;MQ0=0;MQRankSum=-4.804;QD=5.41;ReadPosRankSum=-0.442;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,21:97:99:553,0,2671
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|
|
3511 chr1 135443 . C T 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.451;DP=97;Dels=0.00;FS=2.004;HaplotypeScore=60.8069;MLEAC=1;MLEAF=0.500;MQ=56.90;MQ0=0;MQRankSum=-4.533;QD=5.00;ReadPosRankSum=-0.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,21:97:99:513,0,2730
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|
|
3512 chr1 135446 . C T 1257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.176;DP=97;Dels=0.00;FS=2.653;HaplotypeScore=42.8139;MLEAC=1;MLEAF=0.500;MQ=56.90;MQ0=0;MQRankSum=-7.372;QD=12.97;ReadPosRankSum=-0.666;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:55,42:97:99:1286,0,1882
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|
|
3513 chr1 135450 . C T 1233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.600;DP=94;Dels=0.00;FS=2.740;HaplotypeScore=39.6045;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=0;MQRankSum=-7.169;QD=13.13;ReadPosRankSum=-0.593;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:54,40:94:99:1262,0,1853
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|
|
3514 chr1 135469 . C T 1458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.242;DP=101;Dels=0.00;FS=3.736;HaplotypeScore=21.2632;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=-8.200;QD=14.44;ReadPosRankSum=0.317;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:55,46:101:99:1487,0,1800
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|
|
3515 chr1 135483 . A C 2726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.152;DP=96;Dels=0.00;FS=0.981;HaplotypeScore=66.5358;MLEAC=1;MLEAF=0.500;MQ=56.79;MQ0=0;MQRankSum=-3.811;QD=28.40;ReadPosRankSum=0.230;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,75:96:99:2755,0,482
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|
3516 chr1 135489 . T G 1566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.993;DP=97;Dels=0.00;FS=12.274;HaplotypeScore=43.2734;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=0;MQRankSum=-7.619;QD=16.15;ReadPosRankSum=1.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,47:97:99:1595,0,1719
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|
3517 chr1 135492 . A G 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.233;DP=97;Dels=0.00;FS=1.972;HaplotypeScore=44.2721;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=0;MQRankSum=-4.134;QD=6.52;ReadPosRankSum=0.715;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:73,24:97:99:661,0,2654
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|
|
3518 chr1 135504 . C T 1475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.723;DP=98;Dels=0.00;FS=21.343;HaplotypeScore=21.9832;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=0;MQRankSum=-6.623;QD=15.06;ReadPosRankSum=2.581;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,45:98:99:1504,0,1796
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|
3519 chr1 135514 . T A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.982;DP=97;Dels=0.00;FS=12.661;HaplotypeScore=41.9659;MLEAC=1;MLEAF=0.500;MQ=56.88;MQ0=0;MQRankSum=-5.004;QD=6.73;ReadPosRankSum=0.614;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:73,24:97:99:681,0,2606
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|
3520 chr1 135517 . C T 1587.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.502;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=21.9725;MLEAC=1;MLEAF=0.500;MQ=56.95;MQ0=0;MQRankSum=2.170;QD=16.71;ReadPosRankSum=1.418;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:47,48:95:99:1616,0,1560
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|
3521 chr1 135526 . T G 3368.77 . AC=2;AF=1.00;AN=2;DP=85;Dels=0.00;FS=0.000;HaplotypeScore=53.9823;MLEAC=2;MLEAF=1.00;MQ=57.70;MQ0=0;QD=26.71;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,85:85:99:3397,256,0
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|
|
3522 chr1 135527 . T C 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.045;DP=85;Dels=0.00;FS=8.852;HaplotypeScore=80.9742;MLEAC=1;MLEAF=0.500;MQ=57.70;MQ0=0;MQRankSum=-4.243;QD=2.79;ReadPosRankSum=1.642;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,13:85:99:265,0,2552
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|
|
3523 chr1 135535 . G A 252.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.892;DP=82;Dels=0.00;FS=8.551;HaplotypeScore=39.9876;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=-5.078;QD=3.08;ReadPosRankSum=1.676;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:69,13:82:99:281,0,2484
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|
|
3524 chr1 135536 . C T 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.212;DP=79;Dels=0.00;FS=4.308;HaplotypeScore=39.9876;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=-1.623;QD=4.20;ReadPosRankSum=1.137;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:52,14:79:99:360,0,1863
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|
|
3525 chr1 135537 . A G 868.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.307;DP=78;Dels=0.00;FS=9.867;HaplotypeScore=39.9876;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-4.630;QD=11.14;ReadPosRankSum=1.297;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,28:78:99:897,0,1742
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|
|
3526 chr1 135551 . G A 749.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.458;DP=91;Dels=0.00;FS=9.889;HaplotypeScore=1.9986;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=0;MQRankSum=-4.719;QD=8.24;ReadPosRankSum=-1.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:63,27:91:99:778,0,2232
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|
|
3527 chr1 135557 . A C 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.109;DP=92;Dels=0.00;FS=11.651;HaplotypeScore=3.9926;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-3.944;QD=8.20;ReadPosRankSum=-1.158;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:65,27:92:99:783,0,2240
|
|
|
3528 chr1 135582 . G A 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.013;DP=97;Dels=0.00;FS=10.159;HaplotypeScore=29.4167;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-4.142;QD=6.48;ReadPosRankSum=2.534;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,24:97:99:657,0,2497
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|
|
3529 chr1 135587 . G C 2286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.678;DP=96;Dels=0.00;FS=0.869;HaplotypeScore=28.5846;MLEAC=1;MLEAF=0.500;MQ=58.98;MQ0=0;MQRankSum=0.144;QD=23.82;ReadPosRankSum=0.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,67:96:99:2315,0,856
|
|
|
3530 chr1 135606 . C A 458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.585;DP=96;Dels=0.00;FS=2.045;HaplotypeScore=21.9828;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-0.629;QD=4.78;ReadPosRankSum=0.434;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,21:96:99:487,0,2576
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|
|
3531 chr1 135609 . C A 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.944;DP=93;Dels=0.00;FS=7.797;HaplotypeScore=83.8468;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=-3.424;QD=7.92;ReadPosRankSum=-0.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:66,27:93:99:765,0,2259
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|
|
3532 chr1 135618 . C T 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.853;DP=89;Dels=0.00;FS=1.036;HaplotypeScore=65.8507;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=1.727;QD=3.94;ReadPosRankSum=2.134;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,17:89:99:379,0,2429
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|
|
3533 chr1 135632 . G C 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.374;DP=89;Dels=0.00;FS=3.725;HaplotypeScore=67.7422;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-1.496;QD=4.58;ReadPosRankSum=-0.189;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:71,18:89:99:436,0,2397
|
|
|
3534 chr1 135636 . T C 2955.77 . AC=2;AF=1.00;AN=2;DP=79;Dels=0.00;FS=0.000;HaplotypeScore=82.6805;MLEAC=2;MLEAF=1.00;MQ=58.77;MQ0=0;QD=24.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,78:79:99:2984,226,0
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|
|
3535 chr1 135637 . A C 1811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.105;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=83.6799;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-0.341;QD=22.65;ReadPosRankSum=-0.215;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,56:80:99:1840,0,664
|
|
|
3536 chr1 135639 . T G 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.448;DP=83;Dels=0.00;FS=11.996;HaplotypeScore=104.6691;MLEAC=1;MLEAF=0.500;MQ=58.83;MQ0=0;MQRankSum=-0.923;QD=4.39;ReadPosRankSum=0.569;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:65,18:83:99:393,0,2312
|
|
|
3537 chr1 135641 . C T 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.688;DP=86;Dels=0.00;FS=7.119;HaplotypeScore=129.6566;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=2.648;QD=6.67;ReadPosRankSum=-0.401;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:64,22:86:99:602,0,2169
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|
|
3538 chr1 135642 . C T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.688;DP=86;Dels=0.00;FS=7.119;HaplotypeScore=129.6566;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=2.954;QD=6.71;ReadPosRankSum=-0.144;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:64,22:86:99:605,0,2180
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|
|
3539 chr1 135643 . C T 377.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=90;Dels=0.00;FS=9.549;HaplotypeScore=115.6735;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=-2.215;QD=4.20;ReadPosRankSum=0.801;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:71,19:90:99:406,0,2519
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|
|
3540 chr1 135648 . G C 605.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.143;DP=94;Dels=0.00;FS=0.939;HaplotypeScore=81.8473;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-1.363;QD=6.44;ReadPosRankSum=-0.062;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:71,23:94:99:634,0,2439
|
|
|
3541 chr1 135650 . G A 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.629;DP=98;Dels=0.00;FS=0.925;HaplotypeScore=85.9035;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.805;QD=6.04;ReadPosRankSum=0.553;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,23:98:99:620,0,2541
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|
|
3542 chr1 135660 . T G 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.004;DP=101;Dels=0.00;FS=0.897;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.059;QD=6.71;ReadPosRankSum=0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,25:101:99:706,0,2603
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|
|
3543 chr1 135662 . T C 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=1.122;QD=6.70;ReadPosRankSum=0.532;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,26:101:99:705,0,2524
|
|
|
3544 chr1 135693 . G A 727.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.518;DP=102;Dels=0.00;FS=1.895;HaplotypeScore=1.7219;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=1.915;QD=7.13;ReadPosRankSum=1.270;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:74,28:102:99:756,0,2603
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|
|
3545 chr1 135705 . C T 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.990;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=1;MQRankSum=0.990;QD=6.44;ReadPosRankSum=0.400;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,26:103:99:692,0,2558
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|
|
3546 chr1 135724 . G A 3782.77 . AC=2;AF=1.00;AN=2;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=12.9950;MLEAC=2;MLEAF=1.00;MQ=58.30;MQ0=1;QD=35.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,97:97:99:3811,286,0
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|
|
3547 chr1 135725 . C A 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.036;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=12.9950;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=2;MQRankSum=0.224;QD=6.62;ReadPosRankSum=0.224;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:73,25:98:99:677,0,2539
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|
|
3548 chr1 135734 . C T 217.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.312;DP=84;Dels=0.00;FS=9.368;HaplotypeScore=43.9728;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=3;MQRankSum=-0.578;QD=2.59;ReadPosRankSum=1.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,12:84:99:246,0,2508
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|
|
3549 chr1 135736 . C G 2208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.981;DP=87;Dels=0.00;FS=2.092;HaplotypeScore=32.9825;MLEAC=1;MLEAF=0.500;MQ=56.82;MQ0=3;MQRankSum=-1.198;QD=25.39;ReadPosRankSum=-0.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,66:87:99:2237,0,546
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|
|
3550 chr1 135750 . A G 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.586;DP=76;Dels=0.00;FS=5.360;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.60;MQ0=3;MQRankSum=-1.757;QD=1.50;ReadPosRankSum=2.431;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:66,10:76:99:142,0,2292
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|
|
3551 chr1 135758 . G T 393.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.643;DP=79;Dels=0.00;FS=5.453;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.66;MQ0=3;MQRankSum=-3.574;QD=4.98;ReadPosRankSum=-1.937;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,18:79:99:422,0,2063
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|
|
3552 chr1 135778 . C T 195.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.029;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=-4.222;QD=5.93;ReadPosRankSum=2.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,8:33:99:224,0,882
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|
|
3553 chr1 135782 . G T 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.307;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.47;MQ0=0;MQRankSum=-3.992;QD=5.41;ReadPosRankSum=3.567;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,7:31:99:196,0,843
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|
|
3554 chr1 135800 . C T 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.440;DP=36;Dels=0.00;FS=3.702;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=-4.077;QD=3.97;ReadPosRankSum=1.519;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,7:36:99:171,0,1061
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|
|
3555 chr1 135819 . T C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.242;DP=52;Dels=0.00;FS=6.289;HaplotypeScore=11.8640;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=0;MQRankSum=-1.616;QD=8.25;ReadPosRankSum=-2.282;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:37,15:52:99:457,0,1294
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|
|
3556 chr1 135828 . C T 230.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.663;DP=51;Dels=0.00;FS=8.174;HaplotypeScore=22.8565;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=1.593;QD=4.52;ReadPosRankSum=-0.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:39,11:51:99:259,0,1414
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|
|
3557 chr1 135836 . G T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.890;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=12.5980;MLEAC=1;MLEAF=0.500;MQ=58.80;MQ0=0;MQRankSum=4.353;QD=12.80;ReadPosRankSum=2.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,24:60:99:796,0,1231
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|
|
3558 chr1 135848 . G A 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.467;DP=64;Dels=0.00;FS=2.112;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.656;QD=13.62;ReadPosRankSum=-1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,28:64:99:900,0,1249
|
|
|
3559 chr1 135855 . T G 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.541;DP=69;Dels=0.00;FS=0.917;HaplotypeScore=17.9912;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=1.635;QD=13.33;ReadPosRankSum=-2.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,29:69:99:948,0,1381
|
|
|
3560 chr1 135865 . T C 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.418;DP=67;Dels=0.00;FS=2.217;HaplotypeScore=55.9758;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=-0.993;QD=8.09;ReadPosRankSum=0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:47,20:67:99:570,0,1674
|
|
|
3561 chr1 135868 . A T 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.045;DP=65;Dels=0.00;FS=1.000;HaplotypeScore=20.9924;MLEAC=1;MLEAF=0.500;MQ=58.17;MQ0=0;MQRankSum=1.676;QD=9.50;ReadPosRankSum=1.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:44,21:65:99:646,0,1554
|
|
|
3562 chr1 135874 . T C 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.590;DP=70;Dels=0.00;FS=0.954;HaplotypeScore=19.9927;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=-2.097;QD=10.60;ReadPosRankSum=-0.176;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F2S|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:44,26:70:99:770,0,1499
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|
|
3563 chr1 135880 . T G 690.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.422;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=58.19;MQ0=0;MQRankSum=-1.102;QD=10.01;ReadPosRankSum=0.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F4C|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:45,24:69:99:719,0,1540
|
|
|
3564 chr1 135884 . T C 701.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.749;DP=70;Dels=0.00;FS=2.105;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=-0.179;QD=10.03;ReadPosRankSum=1.132;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H5|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:46,24:70:99:730,0,1622
|
|
|
3565 chr1 135900 . C T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.045;DP=74;Dels=0.00;FS=1.994;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=57.68;MQ0=0;MQRankSum=-0.685;QD=10.38;ReadPosRankSum=0.404;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R11*|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:47,27:74:99:796,0,1573
|
|
|
3566 chr1 135922 . T C 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=92;Dels=0.00;FS=1.814;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-1.479;QD=9.52;ReadPosRankSum=0.760;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I18T|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,31:92:99:904,0,2103
|
|
|
3567 chr1 135936 . A G 764.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.153;DP=84;Dels=0.00;FS=4.645;HaplotypeScore=25.8884;MLEAC=1;MLEAF=0.500;MQ=58.05;MQ0=0;MQRankSum=1.810;QD=9.10;ReadPosRankSum=-0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T23A|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:57,27:84:99:793,0,1944
|
|
|
3568 chr1 135937 . C T 1766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.525;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=25.8884;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=1.487;QD=21.55;ReadPosRankSum=-0.188;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T23I|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,52:82:99:1795,0,896
|
|
|
3569 chr1 135938 . A G 1781.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.486;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=25.8884;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=1.699;QD=21.73;ReadPosRankSum=-0.255;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T23|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,52:82:99:1810,0,895
|
|
|
3570 chr1 135950 . G A 807.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.094;DP=83;Dels=0.00;FS=4.423;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=0.851;QD=9.73;ReadPosRankSum=-0.919;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K27|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:56,27:83:99:836,0,1943
|
|
|
3571 chr1 135990 . T G 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.534;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=18.3925;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=-0.628;QD=8.58;ReadPosRankSum=0.831;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:46,21:67:99:603,0,1660
|
|
|
3572 chr1 135994 . A T 2749.77 . AC=2;AF=1.00;AN=2;DP=70;Dels=0.00;FS=0.000;HaplotypeScore=1.3990;MLEAC=2;MLEAF=1.00;MQ=58.86;MQ0=0;QD=31.63;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,70:70:99:2778,211,0
|
|
|
3573 chr1 136009 . C T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.369;DP=44;Dels=0.00;FS=6.444;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.106;QD=14.20;ReadPosRankSum=-2.510;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:653,0,848
|
|
|
3574 chr1 136065 . A T 567.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.637;DP=46;Dels=0.00;FS=1.150;HaplotypeScore=1.7675;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.035;QD=12.34;ReadPosRankSum=1.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,18:46:99:596,0,963
|
|
|
3575 chr1 136086 . G A 615.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.177;DP=51;Dels=0.00;FS=2.381;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-1.043;QD=12.07;ReadPosRankSum=0.565;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,21:51:99:644,0,1054
|
|
|
3576 chr1 136090 . A G 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.098;DP=50;Dels=0.00;FS=2.463;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=-1.042;QD=12.52;ReadPosRankSum=-0.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:654,0,1012
|
|
|
3577 chr1 136102 . G A 1209.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.676;DP=59;Dels=0.00;FS=2.203;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.365;QD=20.50;ReadPosRankSum=0.179;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,36:59:99:1238,0,690
|
|
|
3578 chr1 136134 . C T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.488;DP=52;Dels=0.00;FS=11.273;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=1.346;QD=8.28;ReadPosRankSum=1.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:35,17:52:99:459,0,1143
|
|
|
3579 chr1 136138 . C T 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.276;DP=53;Dels=0.00;FS=12.293;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=-0.829;QD=7.34;ReadPosRankSum=1.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,17:53:99:417,0,1249
|
|
|
3580 chr1 136150 . G C 528.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.335;DP=51;Dels=0.00;FS=10.821;HaplotypeScore=17.3638;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=-0.945;QD=10.37;ReadPosRankSum=-0.263;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:32,19:51:99:557,0,1120
|
|
|
3581 chr1 136165 . A G 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.333;DP=49;Dels=0.00;FS=8.545;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=-0.736;QD=9.87;ReadPosRankSum=0.238;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:512,0,993
|
|
|
3582 chr1 136178 . C T 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.591;DP=49;Dels=0.00;FS=8.560;HaplotypeScore=1.9248;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-2.250;QD=9.83;ReadPosRankSum=-0.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:510,0,1040
|
|
|
3583 chr1 136208 . G A 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.664;DP=40;Dels=0.00;FS=5.407;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.65;MQ0=0;MQRankSum=-2.022;QD=7.12;ReadPosRankSum=-0.723;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,12:40:99:313,0,1004
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|
|
3584 chr1 136237 . T A 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.248;DP=35;Dels=0.03;FS=1.803;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-1.694;QD=3.25;ReadPosRankSum=1.152;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,6:34:99:142,0,1006
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|
|
3585 chr1 136238 . T A 110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.197;DP=35;Dels=0.03;FS=1.803;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-1.423;QD=3.16;ReadPosRankSum=1.242;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,6:34:99:139,0,998
|
|
|
3586 chr1 136245 . A G 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.130;DP=38;Dels=0.00;FS=1.534;HaplotypeScore=2.9328;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-0.151;QD=3.26;ReadPosRankSum=1.280;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,7:38:99:152,0,1108
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|
|
3587 chr1 136246 . G A 128.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.582;DP=38;Dels=0.00;FS=1.534;HaplotypeScore=2.9328;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-1.054;QD=3.39;ReadPosRankSum=1.393;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,7:38:99:157,0,1099
|
|
|
3588 chr1 136281 . A G 1035.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.637;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=2.132;QD=20.72;ReadPosRankSum=1.081;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,32:50:99:1064,0,533
|
|
|
3589 chr1 136286 . T A 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.044;DP=50;Dels=0.00;FS=1.154;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=1.147;QD=9.96;ReadPosRankSum=-0.430;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:526,0,1136
|
|
|
3590 chr1 136296 . T C 498.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.294;DP=57;Dels=0.00;FS=2.395;HaplotypeScore=1.7870;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.166;QD=8.75;ReadPosRankSum=1.526;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,17:57:99:527,0,1372
|
|
|
3591 chr1 136297 . A C 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.927;DP=57;Dels=0.00;FS=1.124;HaplotypeScore=1.7870;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.951;QD=8.80;ReadPosRankSum=1.788;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,17:57:99:530,0,1359
|
|
|
3592 chr1 136349 . A G 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.221;DP=55;Dels=0.00;FS=4.256;HaplotypeScore=2.8244;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.501;QD=7.32;ReadPosRankSum=-2.806;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,15:55:99:431,0,1458
|
|
|
3593 chr1 136355 . G A 2168.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=2.7122;MLEAC=2;MLEAF=1.00;MQ=59.70;MQ0=0;QD=25.36;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2197,163,0
|
|
|
3594 chr1 136407 . T A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.022;DP=36;Dels=0.00;FS=1.438;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=55.10;MQ0=0;MQRankSum=-4.739;QD=7.63;ReadPosRankSum=1.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,11:36:99:303,0,897
|
|
|
3595 chr1 136411 . G A 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.363;DP=35;Dels=0.00;FS=3.074;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.96;MQ0=0;MQRankSum=-4.708;QD=7.94;ReadPosRankSum=1.723;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,11:35:99:306,0,864
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|
|
3596 chr1 136414 . A G 279.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.761;DP=34;Dels=0.00;FS=1.456;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-4.675;QD=8.23;ReadPosRankSum=1.951;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,11:34:99:308,0,808
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|
|
3597 chr1 136416 . G A 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.470;DP=33;Dels=0.00;FS=1.475;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.63;MQ0=0;MQRankSum=-4.640;QD=8.57;ReadPosRankSum=1.814;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,11:33:99:311,0,783
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3598 chr1 136425 . A G 454.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.487;DP=37;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.86;MQ0=0;MQRankSum=-5.166;QD=12.29;ReadPosRankSum=0.966;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:483,0,735
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|
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3599 chr1 136429 . G A 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.972;DP=39;Dels=0.00;FS=6.978;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.85;MQ0=0;MQRankSum=-5.339;QD=12.84;ReadPosRankSum=0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:529,0,713
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|
|
3600 chr1 136439 . C T 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.524;DP=42;Dels=0.00;FS=8.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.51;MQ0=0;MQRankSum=-5.553;QD=13.61;ReadPosRankSum=0.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A37V|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:600,0,750
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3601 chr1 136450 . C G 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.709;DP=44;Dels=0.00;FS=8.887;HaplotypeScore=14.9765;MLEAC=1;MLEAF=0.500;MQ=51.92;MQ0=0;MQRankSum=-5.669;QD=12.77;ReadPosRankSum=0.884;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Gat|H41D|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:590,0,832
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|
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3602 chr1 136462 . G A 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.861;DP=37;Dels=0.00;FS=5.041;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=51.93;MQ0=0;MQRankSum=-4.995;QD=9.59;ReadPosRankSum=1.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E45K|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:383,0,810
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|
|
3603 chr1 136465 . T A 396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.278;DP=36;Dels=0.00;FS=5.077;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.37;MQ0=0;MQRankSum=-5.070;QD=11.02;ReadPosRankSum=1.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),STOP_LOST(HIGH|MISSENSE|Tga/Aga|*46R|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:425,0,704
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|
|
3604 chr1 136487 . G T 332.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.041;DP=39;Dels=0.00;FS=7.323;HaplotypeScore=1.9787;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-5.050;QD=8.53;ReadPosRankSum=1.475;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:361,0,895
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|
|
3605 chr1 136488 . T C 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.143;DP=39;Dels=0.00;FS=7.323;HaplotypeScore=1.9787;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-5.050;QD=8.66;ReadPosRankSum=1.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:366,0,788
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|
3606 chr1 136547 . A G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.519;DP=52;Dels=0.00;FS=24.103;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=1;MQRankSum=0.123;QD=15.98;ReadPosRankSum=1.840;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I7M|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:24,28:52:99:859,0,785
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3607 chr1 136596 . A C 975.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.509;DP=52;Dels=0.00;FS=1.083;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-0.139;QD=18.76;ReadPosRankSum=-0.917;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Cag|K24Q|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1004,0,696
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3608 chr1 136655 . T A 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.512;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=0.278;QD=15.84;ReadPosRankSum=1.301;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caA|H43Q|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:18,20:38:99:630,0,576
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3609 chr1 136658 . A G 1300.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.42;MQ0=0;QD=31.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I44M|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1329,102,0
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3610 chr1 136742 . C T 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.161;DP=48;Dels=0.00;FS=11.641;HaplotypeScore=1.8937;MLEAC=1;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=0.635;QD=17.29;ReadPosRankSum=-0.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F72|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:20,27:48:99:858,0,624
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|
3611 chr1 136752 . C T 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=43;Dels=0.00;FS=4.498;HaplotypeScore=1.8940;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-1.528;QD=15.37;ReadPosRankSum=0.379;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P76S|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:19,24:43:99:689,0,591
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3612 chr1 136754 . T C 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.739;DP=45;Dels=0.00;FS=8.549;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-0.808;QD=15.51;ReadPosRankSum=1.172;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P76|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,24:45:99:726,0,665
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3613 chr1 136841 . A G 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.684;DP=46;Dels=0.00;FS=2.588;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.110;QD=17.34;ReadPosRankSum=0.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E105|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,25:46:99:826,0,691
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3614 chr1 136898 . A G 1598.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=3.1864;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E124|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1627,126,0
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3615 chr1 136902 . T C 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.935;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=3.1864;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.194;QD=13.13;ReadPosRankSum=-0.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L126|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:25,20:46:99:632,0,609
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3616 chr1 136996 . A G 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.101;DP=42;Dels=0.00;FS=1.141;HaplotypeScore=2.5774;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=1.082;QD=14.73;ReadPosRankSum=0.402;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K157R|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,21:42:99:647,0,707
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|
3617 chr1 137035 . T C 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.509;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.623;QD=14.32;ReadPosRankSum=1.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V170A|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:29,27:56:99:830,0,902
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3618 chr1 137064 . G A 1076.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.151;DP=65;Dels=0.00;FS=3.370;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.846;QD=16.57;ReadPosRankSum=0.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V180I|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:32,33:65:99:1105,0,993
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3619 chr1 137119 . A G 1116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=59;Dels=0.00;FS=0.985;HaplotypeScore=3.6004;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-1.388;QD=18.93;ReadPosRankSum=-0.008;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N198S|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:25,34:59:99:1145,0,816
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3620 chr1 137153 . A G 972.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.416;DP=55;Dels=0.00;FS=2.329;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=1;MQRankSum=2.932;QD=17.69;ReadPosRankSum=-0.885;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S209|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,29:55:99:1001,0,825
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3621 chr1 137179 . A G 799.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.118;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=1.7878;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=1;MQRankSum=-3.289;QD=13.79;ReadPosRankSum=-0.603;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E218G|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:32,26:58:99:828,0,1091
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|
3622 chr1 137275 . G A 1116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.099;DP=55;Dels=0.00;FS=4.048;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=56.44;MQ0=1;MQRankSum=-2.535;QD=20.30;ReadPosRankSum=0.922;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R250K|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:20,35:55:99:1145,0,643
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3623 chr1 137372 . C T 1000.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.535;DP=73;Dels=0.00;FS=1.936;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-0.028;QD=13.71;ReadPosRankSum=0.349;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V282|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:40,33:73:99:1029,0,1332
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|
3624 chr1 137373 . A G 1056.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=73;Dels=0.00;FS=1.936;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-2.632;QD=14.48;ReadPosRankSum=0.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T283A|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:40,33:73:99:1085,0,1343
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|
3625 chr1 137483 . G A 453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.443;DP=39;Dels=0.00;FS=1.238;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.97;MQ0=0;MQRankSum=-0.043;QD=11.64;ReadPosRankSum=-0.043;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M319I|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:23,16:39:99:482,0,810
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|
|
3626 chr1 137571 . A G 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.393;DP=61;Dels=0.00;FS=1.046;HaplotypeScore=1.9787;MLEAC=1;MLEAF=0.500;MQ=55.97;MQ0=0;MQRankSum=-2.341;QD=13.06;ReadPosRankSum=-0.022;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N349D|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:35,26:61:99:825,0,1208
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|
|
3627 chr1 137613 . C T 845.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.184;DP=57;Dels=0.00;FS=4.341;HaplotypeScore=3.9492;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=-2.620;QD=14.84;ReadPosRankSum=-0.665;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L363F|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:31,26:57:99:874,0,1052
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|
|
3628 chr1 137666 . C T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.663;DP=44;Dels=0.00;FS=1.184;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=52.01;MQ0=0;MQRankSum=-0.687;QD=17.20;ReadPosRankSum=1.422;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C380|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:19,25:44:99:785,0,643
|
|
|
3629 chr1 137873 . T C 798.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.28;MQ0=0;MQRankSum=-1.416;QD=15.98;ReadPosRankSum=0.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V449|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:25,25:50:99:827,0,840
|
|
|
3630 chr1 137891 . C T 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.155;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=53.27;MQ0=0;MQRankSum=1.660;QD=16.26;ReadPosRankSum=1.350;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I455|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:24,26:50:99:841,0,766
|
|
|
3631 chr1 137927 . A T 720.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.977;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.75;MQ0=0;MQRankSum=-4.120;QD=12.43;ReadPosRankSum=-0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccT|P467|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:32,26:58:99:749,0,1114
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|
|
3632 chr1 138034 . T C 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.586;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.8939;MLEAC=1;MLEAF=0.500;MQ=53.14;MQ0=0;MQRankSum=0.781;QD=7.54;ReadPosRankSum=-1.513;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V503A|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:33,13:46:99:375,0,1176
|
|
|
3633 chr1 138075 . C T 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.293;DP=48;Dels=0.00;FS=2.557;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=48.83;MQ0=0;MQRankSum=-4.500;QD=14.02;ReadPosRankSum=-0.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L517|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,22:48:99:701,0,894
|
|
|
3634 chr1 138170 . A G 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.530;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=54.39;MQ0=0;MQRankSum=-3.956;QD=13.84;ReadPosRankSum=-0.258;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K548|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:22,18:40:99:582,0,750
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|
|
3635 chr1 138221 . G A 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.402;DP=49;Dels=0.00;FS=4.125;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=53.04;MQ0=0;MQRankSum=-4.650;QD=14.73;ReadPosRankSum=1.474;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K565|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:24,24:49:99:750,0,740
|
|
|
3636 chr1 138281 . C T 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.653;DP=47;Dels=0.00;FS=8.620;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=-4.611;QD=12.82;ReadPosRankSum=0.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T585|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,21:47:99:631,0,882
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|
|
3637 chr1 138362 . T C 690.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.377;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.11;MQ0=0;MQRankSum=-3.648;QD=16.45;ReadPosRankSum=0.302;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A612|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,21:42:99:719,0,680
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|
|
3638 chr1 138386 . T C 665.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.181;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-3.153;QD=15.48;ReadPosRankSum=0.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F620|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:23,20:43:99:694,0,739
|
|
|
3639 chr1 138609 . G A 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.214;DP=50;Dels=0.00;FS=3.842;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=48.15;MQ0=0;MQRankSum=-4.884;QD=12.04;ReadPosRankSum=0.573;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E695K|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,24:50:99:630,0,897
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|
|
3640 chr1 138660 . C A 981.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.269;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.11;MQ0=0;MQRankSum=4.417;QD=18.88;ReadPosRankSum=0.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1010,0,467
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|
|
3641 chr1 138683 . G T 559.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.363;DP=56;Dels=0.00;FS=2.284;HaplotypeScore=2.8620;MLEAC=1;MLEAF=0.500;MQ=46.57;MQ0=0;MQRankSum=-4.417;QD=10.00;ReadPosRankSum=-2.357;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:588,0,1019
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|
|
3642 chr1 138698 . T C 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.649;DP=58;Dels=0.00;FS=2.144;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.13;MQ0=0;MQRankSum=-3.995;QD=10.77;ReadPosRankSum=-1.900;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:653,0,1080
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|
|
3643 chr1 138718 . T C 720.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.205;DP=53;Dels=0.00;FS=5.608;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.57;MQ0=0;MQRankSum=-4.422;QD=13.60;ReadPosRankSum=-0.348;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:749,0,948
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|
|
3644 chr1 138736 . T C 816.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.990;DP=50;Dels=0.00;FS=10.029;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.58;MQ0=0;MQRankSum=-4.540;QD=16.34;ReadPosRankSum=-0.136;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:845,0,811
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|
|
3645 chr1 138777 . T A 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.575;DP=53;Dels=0.00;FS=2.347;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=52.94;MQ0=0;MQRankSum=-4.937;QD=16.24;ReadPosRankSum=-1.005;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,26:53:99:889,0,952
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|
3646 chr1 138778 . C T 2144.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9958;MLEAC=2;MLEAF=1.00;MQ=52.94;MQ0=0;QD=33.40;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2173,163,0
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|
|
3647 chr1 138820 . A C 2124.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.95;MQ0=0;QD=31.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2153,160,0
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|
|
3648 chr1 138922 . A T 728.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.417;DP=57;Dels=0.00;FS=1.039;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=51.61;MQ0=1;MQRankSum=-0.363;QD=12.79;ReadPosRankSum=-1.187;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:757,0,1026
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|
|
3649 chr1 138960 . T C 2157.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.52;MQ0=1;QD=28.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2186,172,0
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|
|
3650 chr1 138982 . C A 1007.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.642;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=51.16;MQ0=1;MQRankSum=0.793;QD=17.38;ReadPosRankSum=0.248;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,32:58:99:1036,0,849
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|
|
3651 chr1 139024 . A T 1024.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.725;DP=56;Dels=0.00;FS=5.451;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.72;MQ0=0;MQRankSum=-1.928;QD=18.30;ReadPosRankSum=0.478;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,31:56:99:1053,0,858
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|
|
3652 chr1 139066 . A G 959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.886;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=0;MQRankSum=-3.328;QD=16.55;ReadPosRankSum=-0.622;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,29:58:99:988,0,1020
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|
|
3653 chr1 139093 . A G 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.500;DP=47;Dels=0.00;FS=4.452;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.31;MQ0=0;MQRankSum=-4.267;QD=16.85;ReadPosRankSum=-1.245;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:820,0,809
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|
|
3654 chr1 139143 . A G 667.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.629;DP=38;Dels=0.00;FS=2.742;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.86;MQ0=0;MQRankSum=-4.926;QD=17.57;ReadPosRankSum=1.973;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,20:38:99:696,0,605
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|
|
3655 chr1 139149 . A G 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.294;DP=38;Dels=0.00;FS=2.835;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.61;MQ0=0;MQRankSum=-4.932;QD=18.23;ReadPosRankSum=1.233;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:17,21:38:99:721,0,567
|
|
|
3656 chr1 139163 . C T 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.604;DP=39;Dels=0.00;FS=6.884;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.85;MQ0=0;MQRankSum=-5.156;QD=14.30;ReadPosRankSum=1.391;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:586,0,689
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|
|
3657 chr1 139224 . A G 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.302;DP=58;Dels=0.00;FS=3.833;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=-5.755;QD=12.22;ReadPosRankSum=0.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:737,0,1030
|
|
|
3658 chr1 139254 . C T 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.070;DP=60;Dels=0.00;FS=3.815;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.67;MQ0=0;MQRankSum=-4.339;QD=14.35;ReadPosRankSum=-0.594;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,27:60:99:889,0,1036
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|
|
3659 chr1 139269 . A G 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.023;DP=58;Dels=0.00;FS=1.019;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.74;MQ0=0;MQRankSum=-4.651;QD=14.17;ReadPosRankSum=0.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:850,0,1089
|
|
|
3660 chr1 139286 . A G 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.863;DP=56;Dels=0.00;FS=3.856;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.14;MQ0=0;MQRankSum=-3.836;QD=15.19;ReadPosRankSum=0.222;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:879,0,1015
|
|
|
3661 chr1 139341 . A G 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.331;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.17;MQ0=0;MQRankSum=-2.059;QD=15.48;ReadPosRankSum=-0.421;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:725,0,819
|
|
|
3662 chr1 139358 . A T 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.459;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.28;MQ0=0;MQRankSum=-2.238;QD=14.18;ReadPosRankSum=-0.694;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:737,0,962
|
|
|
3663 chr1 139417 . A C 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.696;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.85;MQ0=0;MQRankSum=-5.263;QD=8.24;ReadPosRankSum=-1.884;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:440,0,1164
|
|
|
3664 chr1 139435 . T G 226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.343;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.55;MQ0=0;MQRankSum=-5.052;QD=4.45;ReadPosRankSum=0.944;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:39,12:51:99:255,0,1407
|
|
|
3665 chr1 139441 . G A 262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.092;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.34;MQ0=0;MQRankSum=-5.283;QD=5.05;ReadPosRankSum=0.845;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:39,13:52:99:291,0,1353
|
|
|
3666 chr1 139480 . A G 107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.122;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.50;MQ0=0;MQRankSum=-4.475;QD=2.29;ReadPosRankSum=1.014;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:38,9:47:99:136,0,1324
|
|
|
3667 chr1 139483 . T C 1251.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.548;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.24;MQ0=0;MQRankSum=5.087;QD=25.04;ReadPosRankSum=0.863;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:13,37:50:99:1280,0,278
|
|
|
3668 chr1 139488 . T A 312.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.949;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.71;MQ0=0;MQRankSum=-5.373;QD=6.01;ReadPosRankSum=-1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:37,15:52:99:341,0,1293
|
|
|
3669 chr1 139495 . G T 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.423;DP=50;Dels=0.00;FS=1.248;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=53.45;MQ0=0;MQRankSum=-5.314;QD=6.36;ReadPosRankSum=-1.207;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:346,0,1235
|
|
|
3670 chr1 139501 . T G 297.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.434;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9790;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=-5.063;QD=6.62;ReadPosRankSum=-0.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:326,0,1098
|
|
|
3671 chr1 139502 . A G 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.066;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9790;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=-5.063;QD=6.55;ReadPosRankSum=-0.454;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:323,0,1098
|
|
|
3672 chr1 139534 . T C 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.920;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=51.00;MQ0=0;MQRankSum=-5.026;QD=15.83;ReadPosRankSum=-0.795;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,24:43:99:709,0,616
|
|
|
3673 chr1 139556 . A G 531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.516;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=5.120;QD=12.09;ReadPosRankSum=-2.136;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:560,0,740
|
|
|
3674 chr1 139563 . T C 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.675;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.21;MQ0=0;MQRankSum=-5.014;QD=18.81;ReadPosRankSum=1.928;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:17,27:44:99:856,0,472
|
|
|
3675 chr1 139576 . C A 817.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.257;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=19.9086;MLEAC=1;MLEAF=0.500;MQ=51.06;MQ0=1;MQRankSum=-4.247;QD=21.52;ReadPosRankSum=1.511;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:846,0,350
|
|
|
3676 chr1 139610 . C T 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.376;DP=44;Dels=0.00;FS=11.681;HaplotypeScore=8.3569;MLEAC=1;MLEAF=0.500;MQ=48.86;MQ0=0;MQRankSum=-4.699;QD=13.06;ReadPosRankSum=-1.057;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:603,0,686
|
|
|
3677 chr1 139650 . C A 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.148;DP=45;Dels=0.00;FS=8.659;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.29;MQ0=0;MQRankSum=-3.849;QD=15.37;ReadPosRankSum=0.647;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,23:45:99:720,0,755
|
|
|
3678 chr1 139666 . T A 1813.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=51.90;MQ0=0;QD=29.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,46:47:99:1842,138,0
|
|
|
3679 chr1 139700 . T C 657.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.796;DP=42;Dels=0.00;FS=2.709;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=53.09;MQ0=1;MQRankSum=-4.603;QD=15.66;ReadPosRankSum=-0.743;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:686,0,746
|
|
|
3680 chr1 139730 . T C 609.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.840;DP=44;Dels=0.00;FS=2.648;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.08;MQ0=1;MQRankSum=-5.150;QD=13.86;ReadPosRankSum=0.037;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:638,0,806
|
|
|
3681 chr1 139736 . A G 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.384;DP=47;Dels=0.00;FS=4.288;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=1;MQRankSum=-4.921;QD=13.97;ReadPosRankSum=-0.637;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:685,0,804
|
|
|
3682 chr1 139754 . C T 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.499;DP=44;Dels=0.00;FS=9.774;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=49.58;MQ0=1;MQRankSum=-5.101;QD=14.49;ReadPosRankSum=-0.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:666,0,663
|
|
|
3683 chr1 139766 . T C 545.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.920;DP=47;Dels=0.00;FS=19.585;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.61;MQ0=2;MQRankSum=-4.394;QD=11.61;ReadPosRankSum=0.874;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:574,0,790
|
|
|
3684 chr1 139816 . T A 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=40;Dels=0.00;FS=36.168;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.74;MQ0=1;MQRankSum=3.812;QD=18.44;ReadPosRankSum=0.871;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:16,24:40:99:766,0,353
|
|
|
3685 chr1 139888 . A G 186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.061;DP=34;Dels=0.00;FS=8.801;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.98;MQ0=0;MQRankSum=-4.243;QD=5.49;ReadPosRankSum=-1.319;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,8:34:99:215,0,931
|
|
|
3686 chr1 140035 . C T 1028.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.162;DP=30;Dels=0.03;FS=0.000;HaplotypeScore=5.5143;MLEAC=2;MLEAF=1.00;MQ=56.59;MQ0=0;MQRankSum=1.764;QD=34.29;ReadPosRankSum=-0.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:2,27:29:43:1057,43,0
|
|
|
3687 chr1 140037 . C T 1021.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.347;DP=31;Dels=0.03;FS=0.000;HaplotypeScore=5.5143;MLEAC=2;MLEAF=1.00;MQ=56.70;MQ0=0;MQRankSum=1.271;QD=32.96;ReadPosRankSum=0.924;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:1,29:30:44:1050,44,0
|
|
|
3688 chr1 140066 . A G 1165.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1194,90,0
|
|
|
3689 chr1 140150 . A G 903.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.68;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,24:24:69:932,69,0
|
|
|
3690 chr1 140265 . A T 876.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.93;MQ0=0;QD=24.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:905,69,0
|
|
|
3691 chr1 140358 . G A 1191.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,31:31:90:1220,90,0
|
|
|
3692 chr1 140388 . T C 1024.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.11;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:1053,78,0
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|
|
3693 chr1 140546 . T C 430.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,12:12:36:459,36,0
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|
|
3694 chr1 140560 . T C 561.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.13;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:590,45,0
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|
|
3695 chr1 141091 . G A 812.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=16.5641;MLEAC=2;MLEAF=1.00;MQ=59.48;MQ0=0;QD=32.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:841,63,0
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|
|
3696 chr1 141137 . A G 1166.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,31:32:90:1195,90,0
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|
|
3697 chr1 141143 . C T 1261.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1290,96,0
|
|
|
3698 chr1 141147 . C T 1086.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,31:31:84:1115,84,0
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|
|
3699 chr1 141182 . C G 1085.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1114,84,0
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|
|
3700 chr1 141263 . G A 1101.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1130,84,0
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|
|
3701 chr1 141349 . C T 1090.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.9990;MLEAC=2;MLEAF=1.00;MQ=59.61;MQ0=0;QD=30.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1119,84,0
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|
|
3702 chr1 141378 . T C 1215.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.46;MQ0=0;QD=30.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1244,96,0
|
|
|
3703 chr1 141387 . C T 1141.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.42;MQ0=0;QD=27.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1170,90,0
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|
|
3704 chr1 141396 . C T 955.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;QD=32.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,27:27:75:984,75,0
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|
|
3705 chr1 141400 . T C 1036.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;QD=27.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1065,81,0
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|
|
3706 chr1 141412 . T C 854.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=0;QD=32.36;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:883,66,0
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|
|
3707 chr1 141422 . G A 736.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.42;MQ0=0;QD=28.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,19:20:57:765,57,0
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|
|
3708 chr1 141455 . G A 804.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.72;MQ0=0;QD=26.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:833,63,0
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|
|
3709 chr1 141471 . C T 759.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:788,60,0
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|
|
3710 chr1 141498 . C A 891.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:920,69,0
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|
|
3711 chr1 141507 . G C 961.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,25:25:75:990,75,0
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|
|
3712 chr1 141536 . A G 1066.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1095,81,0
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|
|
3713 chr1 141614 . A T 553.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:582,45,0
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|
|
3714 chr1 141636 . C A 434.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.44;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:463,39,0
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|
|
3715 chr1 141654 . T A 544.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.20;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:573,45,0
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|
|
3716 chr1 141655 . T A 534.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.26;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:563,45,0
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|
|
3717 chr1 142437 . C T 368.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.548;DP=27;Dels=0.00;FS=27.139;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.77;MQ0=0;MQRankSum=-4.440;QD=13.66;ReadPosRankSum=-4.440;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:14,13:27:99:397,0,497
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|
|
3718 chr1 142438 . A G 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.383;DP=27;Dels=0.00;FS=27.139;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.77;MQ0=0;MQRankSum=4.392;QD=16.73;ReadPosRankSum=4.392;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:13,14:27:99:480,0,389
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|
|
3719 chr1 142481 . A G 1079.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.38;MQ0=0;QD=33.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,32:32:90:1108,90,0
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|
|
3720 chr1 142494 . T C 884.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.77;MQ0=0;QD=32.77;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,27:27:75:913,75,0
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|
|
3721 chr1 142601 . A G 2064.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.05;MQ0=0;QD=31.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2093,165,0
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|
|
3722 chr1 142776 . G A 1396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.227;DP=67;Dels=0.00;FS=3.384;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.34;MQ0=0;MQRankSum=-3.183;QD=20.85;ReadPosRankSum=1.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,42:67:99:1425,0,774
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|
|
3723 chr1 142787 . C T 2578.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.71;MQ0=0;QD=24.09;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2607,199,0
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|
|
3724 chr1 142805 . A G 2382.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=2;MLEAF=1.00;MQ=42.75;MQ0=0;QD=29.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,63:63:99:2411,184,0
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|
|
3725 chr1 142821 . T A 1258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.014;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=43.83;MQ0=0;MQRankSum=-1.966;QD=20.30;ReadPosRankSum=-0.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,37:62:99:1287,0,713
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|
|
3726 chr1 142863 . G A 845.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.691;DP=51;Dels=0.00;FS=2.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.90;MQ0=0;MQRankSum=-0.161;QD=16.58;ReadPosRankSum=-0.407;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:874,0,753
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|
|
3727 chr1 142891 . A T 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=53;Dels=0.00;FS=3.828;HaplotypeScore=2.9990;MLEAC=1;MLEAF=0.500;MQ=56.01;MQ0=0;MQRankSum=2.468;QD=17.49;ReadPosRankSum=-0.294;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:955,0,777
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|
|
3728 chr1 142898 . A G 956.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.509;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=0.197;QD=17.09;ReadPosRankSum=0.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,29:56:99:985,0,879
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|
|
3729 chr1 142936 . A C 1403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.302;DP=77;Dels=0.00;FS=0.875;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-0.936;QD=18.23;ReadPosRankSum=-0.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,42:77:99:1432,0,1097
|
|
|
3730 chr1 142944 . T C 1485.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.608;DP=75;Dels=0.00;FS=1.980;HaplotypeScore=1.9788;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.683;QD=19.81;ReadPosRankSum=-1.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,44:75:99:1514,0,922
|
|
|
3731 chr1 142972 . C T 1381.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.788;DP=75;Dels=0.00;FS=0.882;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=1.585;QD=18.42;ReadPosRankSum=1.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,42:75:99:1410,0,1088
|
|
|
3732 chr1 143047 . G C 845.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=57;Dels=0.00;FS=5.471;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=2;MQRankSum=-0.379;QD=14.84;ReadPosRankSum=0.665;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:874,0,913
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|
|
3733 chr1 143077 . G A 615.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.944;DP=43;Dels=0.00;FS=4.575;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=-1.876;QD=14.32;ReadPosRankSum=-0.038;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:644,0,718
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|
|
3734 chr1 143079 . T A 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.790;DP=44;Dels=0.00;FS=6.548;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.05;MQ0=1;MQRankSum=-1.497;QD=13.54;ReadPosRankSum=0.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:624,0,799
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|
|
3735 chr1 143101 . G A 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.221;DP=58;Dels=0.00;FS=5.324;HaplotypeScore=5.2545;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-0.582;QD=15.00;ReadPosRankSum=-0.123;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,28:58:99:898,0,920
|
|
|
3736 chr1 143121 . C T 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.297;DP=78;Dels=0.00;FS=16.462;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=0;MQRankSum=-4.301;QD=1.05;ReadPosRankSum=-3.566;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:69,9:78:99:110,0,2263
|
|
|
3737 chr1 143129 . A G 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.347;DP=82;Dels=0.00;FS=21.866;HaplotypeScore=20.8424;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=0;MQRankSum=-4.844;QD=1.53;ReadPosRankSum=-2.748;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:71,11:82:99:154,0,2388
|
|
|
3738 chr1 143138 . T C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.733;DP=85;Dels=0.00;FS=19.743;HaplotypeScore=26.7703;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=3.325;QD=10.00;ReadPosRankSum=1.658;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:51,34:85:99:878,0,1589
|
|
|
3739 chr1 143140 . C T 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.977;DP=85;Dels=0.00;FS=27.442;HaplotypeScore=15.7969;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=-4.591;QD=3.11;ReadPosRankSum=-1.831;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:71,14:85:99:293,0,2284
|
|
|
3740 chr1 143161 . G A 909.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.080;DP=78;Dels=0.00;FS=0.906;HaplotypeScore=32.9944;MLEAC=1;MLEAF=0.500;MQ=56.48;MQ0=0;MQRankSum=1.886;QD=11.66;ReadPosRankSum=-0.501;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:46,32:78:99:938,0,1383
|
|
|
3741 chr1 143163 . C A 804.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.670;DP=78;Dels=0.00;FS=0.000;HaplotypeScore=33.0925;MLEAC=1;MLEAF=0.500;MQ=56.48;MQ0=0;MQRankSum=3.100;QD=10.32;ReadPosRankSum=-0.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:46,31:78:99:833,0,1525
|
|
|
3742 chr1 143164 . G T 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.056;DP=79;Dels=0.00;FS=32.060;HaplotypeScore=33.8812;MLEAC=1;MLEAF=0.500;MQ=56.53;MQ0=0;MQRankSum=-4.706;QD=4.33;ReadPosRankSum=2.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:64,15:79:99:370,0,2093
|
|
|
3743 chr1 143165 . G A 310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.444;DP=79;Dels=0.00;FS=28.863;HaplotypeScore=33.8812;MLEAC=1;MLEAF=0.500;MQ=56.53;MQ0=0;MQRankSum=-3.856;QD=3.93;ReadPosRankSum=2.881;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:64,15:79:99:339,0,2068
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|
|
3744 chr1 143178 . C A 314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.003;DP=76;Dels=0.00;FS=33.120;HaplotypeScore=44.4775;MLEAC=1;MLEAF=0.500;MQ=56.95;MQ0=0;MQRankSum=-4.295;QD=4.14;ReadPosRankSum=3.343;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:62,14:76:99:343,0,1910
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|
|
3745 chr1 143221 . A T 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.319;DP=63;Dels=0.00;FS=19.029;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=2;MQRankSum=-2.568;QD=1.30;ReadPosRankSum=-0.916;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:54,9:63:99:110,0,1876
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|
|
3746 chr1 143253 . G T 2036.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=58.62;MQ0=0;QD=42.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2065,159,0
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|
|
3747 chr1 143376 . C G 1045.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.421;DP=51;Dels=0.00;FS=6.452;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=55.33;MQ0=6;MQRankSum=2.251;QD=20.51;ReadPosRankSum=-0.229;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,30:51:99:1074,0,461
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|
|
3748 chr1 143406 . G A 740.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=55;Dels=0.00;FS=3.966;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.48;MQ0=2;MQRankSum=-1.903;QD=13.47;ReadPosRankSum=0.759;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:769,0,1020
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|
|
3749 chr1 143414 . A G 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.607;DP=56;Dels=0.00;FS=5.804;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=2;MQRankSum=-0.572;QD=12.89;ReadPosRankSum=1.336;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,27:56:99:750,0,1015
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|
|
3750 chr1 143459 . G T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.432;DP=56;Dels=0.00;FS=5.668;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=2;MQRankSum=1.522;QD=11.17;ReadPosRankSum=0.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:654,0,1069
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|
|
3751 chr1 143490 . A G 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.752;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=-1.155;QD=11.50;ReadPosRankSum=0.052;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:649,0,1103
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|
|
3752 chr1 143531 . G A 1174.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=61;Dels=0.00;FS=2.178;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=0.591;QD=19.26;ReadPosRankSum=1.087;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,35:61:99:1203,0,835
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|
|
3753 chr1 143603 . C T 889.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.678;DP=57;Dels=0.00;FS=3.724;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=-1.269;QD=15.61;ReadPosRankSum=0.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:918,0,950
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|
|
3754 chr1 143650 . T C 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.674;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.267;QD=17.93;ReadPosRankSum=1.209;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:871,0,713
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|
|
3755 chr1 143705 . G A 755.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.934;DP=50;Dels=0.00;FS=10.323;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=1.538;QD=15.12;ReadPosRankSum=0.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:784,0,957
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|
|
3756 chr1 143726 . C T 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.972;DP=51;Dels=0.00;FS=4.147;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=0;MQRankSum=0.349;QD=15.19;ReadPosRankSum=-1.179;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:803,0,907
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|
|
3757 chr1 143837 . A G 851.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.524;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.74;MQ0=0;MQRankSum=-3.207;QD=15.49;ReadPosRankSum=2.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:880,0,915
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|
|
3758 chr1 143843 . G T 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.62;MQ0=0;MQRankSum=-2.653;QD=15.86;ReadPosRankSum=1.953;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:948,0,954
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|
|
3759 chr1 143851 . A T 948.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.281;DP=55;Dels=0.00;FS=2.282;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.36;MQ0=0;MQRankSum=-2.639;QD=17.25;ReadPosRankSum=0.789;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,31:55:99:977,0,823
|
|
|
3760 chr1 143867 . T A 1082.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.451;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=-2.076;QD=17.19;ReadPosRankSum=-0.993;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,36:63:99:1111,0,885
|
|
|
3761 chr1 143879 . A C 1059.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.732;DP=66;Dels=0.00;FS=0.942;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=53.64;MQ0=0;MQRankSum=-1.603;QD=16.06;ReadPosRankSum=-1.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,36:66:99:1088,0,1011
|
|
|
3762 chr1 143887 . C G 1133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.947;DP=70;Dels=0.00;FS=0.918;HaplotypeScore=4.7286;MLEAC=1;MLEAF=0.500;MQ=54.49;MQ0=0;MQRankSum=-0.633;QD=16.20;ReadPosRankSum=-1.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,38:70:99:1162,0,1037
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|
|
3763 chr1 143960 . C T 590.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.036;DP=49;Dels=0.00;FS=2.555;HaplotypeScore=2.8995;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.728;QD=12.06;ReadPosRankSum=-0.811;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:619,0,1001
|
|
|
3764 chr1 144130 . G A 1136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.142;DP=62;Dels=0.00;FS=5.270;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=0.014;QD=18.33;ReadPosRankSum=-1.689;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_3_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:27,35:62:99:1165,0,864
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|
|
3765 chr1 144149 . G A 1000.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.171;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=1.013;QD=17.25;ReadPosRankSum=-1.839;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_3_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1029,0,881
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|
|
3766 chr1 144222 . A G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.156;DP=54;Dels=0.00;FS=5.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.87;MQ0=0;MQRankSum=-2.776;QD=15.38;ReadPosRankSum=-0.729;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R143|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,29:54:99:859,0,804
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|
|
3767 chr1 144255 . A G 844.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.055;DP=54;Dels=0.00;FS=10.821;HaplotypeScore=2.7619;MLEAC=1;MLEAF=0.500;MQ=55.54;MQ0=0;MQRankSum=-5.069;QD=15.64;ReadPosRankSum=1.367;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T132|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,27:54:99:873,0,825
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|
|
3768 chr1 144286 . C G 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.419;DP=45;Dels=0.00;FS=1.238;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=54.87;MQ0=0;MQRankSum=-5.256;QD=15.22;ReadPosRankSum=1.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G122A|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:713,0,730
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|
|
3769 chr1 144294 . T A 757.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.604;DP=46;Dels=0.00;FS=1.253;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=-5.317;QD=16.47;ReadPosRankSum=0.330;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E119D|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:786,0,731
|
|
|
3770 chr1 144318 . G T 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.548;DP=40;Dels=0.00;FS=5.217;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.65;MQ0=0;MQRankSum=-5.240;QD=14.62;ReadPosRankSum=-1.531;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgC/cgA|R111|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:613,0,598
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|
|
3771 chr1 144319 . C T 586.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.068;DP=40;Dels=0.00;FS=2.910;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.74;MQ0=0;MQRankSum=-5.180;QD=14.67;ReadPosRankSum=-1.312;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R111H|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:615,0,628
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|
|
3772 chr1 144346 . G C 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.948;DP=45;Dels=0.00;FS=4.291;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=54.27;MQ0=0;MQRankSum=-4.374;QD=17.19;ReadPosRankSum=0.400;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aGt|T102S|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:802,0,630
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|
|
3773 chr1 144351 . A C 735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.002;DP=48;Dels=0.00;FS=2.471;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=55.03;MQ0=0;MQRankSum=-4.499;QD=15.33;ReadPosRankSum=1.692;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccG|P100|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:764,0,687
|
|
|
3774 chr1 144382 . T G 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.479;DP=53;Dels=0.00;FS=2.371;HaplotypeScore=4.8928;MLEAC=1;MLEAF=0.500;MQ=56.28;MQ0=0;MQRankSum=-2.346;QD=14.58;ReadPosRankSum=2.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gCt|D90A|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,25:53:99:801,0,829
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|
|
3775 chr1 144385 . T C 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.198;DP=52;Dels=0.00;FS=2.379;HaplotypeScore=6.8884;MLEAC=1;MLEAF=0.500;MQ=56.21;MQ0=0;MQRankSum=-2.125;QD=15.05;ReadPosRankSum=2.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D89G|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:811,0,831
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|
|
3776 chr1 144434 . T A 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.026;DP=55;Dels=0.00;FS=1.039;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.232;QD=12.49;ReadPosRankSum=-0.249;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N73Y|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:715,0,1146
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|
|
3777 chr1 144525 . A G 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.018;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.856;QD=18.21;ReadPosRankSum=-0.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R42|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,19:33:99:629,0,394
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|
|
3778 chr1 144561 . C G 729.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.585;DP=39;Dels=0.00;FS=1.238;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.70;MQ0=0;MQRankSum=-0.186;QD=18.71;ReadPosRankSum=1.042;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgG/cgC|R30|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,23:39:99:758,0,482
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|
|
3779 chr1 144564 . C T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.015;DP=37;Dels=0.00;FS=2.870;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=59.69;MQ0=0;MQRankSum=0.541;QD=19.10;ReadPosRankSum=0.943;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q29|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,22:37:99:735,0,466
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|
|
3780 chr1 144576 . C G 1458.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.69;MQ0=0;QD=35.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttC|L25F|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1487,114,0
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|
|
3781 chr1 144606 . G C 868.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.165;DP=54;Dels=0.00;FS=2.347;HaplotypeScore=2.7334;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.276;QD=16.09;ReadPosRankSum=-0.898;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcG|S15|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,27:54:99:897,0,877
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|
|
3782 chr1 144686 . T C 910.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.844;DP=54;Dels=0.00;FS=1.047;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-0.788;QD=16.87;ReadPosRankSum=-1.169;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_5_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887) GT:AD:DP:GQ:PL 0/1:26,28:54:99:939,0,867
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|
|
3783 chr1 144759 . C G 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.336;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.833;QD=14.26;ReadPosRankSum=1.126;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_5_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887) GT:AD:DP:GQ:PL 0/1:20,18:38:99:570,0,686
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|
|
3784 chr1 144778 . G C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.293;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.50;MQ0=0;MQRankSum=-1.949;QD=17.02;ReadPosRankSum=-1.535;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),START_GAINED(LOW||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:607,0,531
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|
|
3785 chr1 144839 . C T 299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.835;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=1.6671;MLEAC=1;MLEAF=0.500;MQ=56.40;MQ0=0;MQRankSum=-3.678;QD=8.56;ReadPosRankSum=-2.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_5_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887) GT:AD:DP:GQ:PL 0/1:24,11:35:99:328,0,819
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|
|
3786 chr1 144896 . C T 1822.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.76;MQ0=0;QD=33.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1851,138,0
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|
3787 chr1 144909 . G A 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.494;DP=44;Dels=0.00;FS=4.590;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=0.603;QD=20.77;ReadPosRankSum=0.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,27:44:99:942,0,494
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|
3788 chr1 144934 . T G 809.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.348;DP=38;Dels=0.00;FS=17.088;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.893;QD=21.31;ReadPosRankSum=1.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:838,0,442
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|
3789 chr1 144950 . G A 844.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.054;DP=38;Dels=0.00;FS=11.386;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-1.801;QD=22.23;ReadPosRankSum=0.762;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,25:38:99:873,0,375
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|
|
3790 chr1 144960 . A G 731.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.762;DP=31;Dels=0.00;FS=13.484;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=0.675;QD=23.61;ReadPosRankSum=-0.762;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,22:31:99:760,0,270
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|
|
3791 chr1 144980 . T G 288.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.632;DP=27;Dels=0.00;FS=10.401;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.879;QD=10.70;ReadPosRankSum=-0.276;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,10:27:99:317,0,537
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|
|
3792 chr1 145002 . C G 240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.075;DP=27;Dels=0.00;FS=10.401;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=0.427;QD=8.92;ReadPosRankSum=0.778;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,10:27:99:269,0,580
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|
|
3793 chr1 145030 . C T 408.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.043;DP=27;Dels=0.00;FS=7.832;HaplotypeScore=1.7465;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=-0.704;QD=15.14;ReadPosRankSum=0.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,13:27:99:437,0,486
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|
|
3794 chr1 145051 . C T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.259;DP=26;Dels=0.00;FS=10.770;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=-0.571;QD=19.38;ReadPosRankSum=-1.038;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:11,15:26:99:532,0,376
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|
|
3795 chr1 145056 . T C 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.860;DP=25;Dels=0.00;FS=10.578;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.248;QD=12.11;ReadPosRankSum=1.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,10:25:99:331,0,511
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|
|
3796 chr1 145062 . C T 1092.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.27;MQ0=0;QD=29.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1121,84,0
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|
|
3797 chr1 145137 . A G 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.333;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=17.5729;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=0;MQRankSum=-3.783;QD=5.84;ReadPosRankSum=-3.420;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,7:26:99:180,0,645
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|
|
3798 chr1 145149 . G C 959.1 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.936;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.9894;MLEAC=2;MLEAF=1.00;MQ=52.35;MQ0=2;MQRankSum=1.244;QD=29.97;ReadPosRankSum=2.005;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:5,27:32:11:987,11,0
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|
|
3799 chr1 145165 . C A 1164.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=50.22;MQ0=3;QD=33.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,35:35:96:1193,96,0
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|
|
3800 chr1 145178 . T A 1075.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.61;MQ0=3;QD=33.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,32:32:87:1104,87,0
|
|
|
3801 chr1 145196 . A T 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.445;DP=31;Dels=0.00;FS=4.262;HaplotypeScore=15.6286;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=3;MQRankSum=-2.370;QD=20.54;ReadPosRankSum=1.908;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,19:31:99:665,0,196
|
|
|
3802 chr1 145230 . A G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=40;Dels=0.00;FS=9.177;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=2;MQRankSum=1.303;QD=8.29;ReadPosRankSum=2.151;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,13:40:99:360,0,901
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|
|
3803 chr1 145381 . T C 837.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.906;DP=37;Dels=0.03;FS=0.000;HaplotypeScore=9.9562;MLEAC=1;MLEAF=0.500;MQ=56.83;MQ0=1;MQRankSum=0.283;QD=22.64;ReadPosRankSum=-0.321;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,27:36:99:866,0,203
|
|
|
3804 chr1 145385 . A T 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.549;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=9.9562;MLEAC=1;MLEAF=0.500;MQ=56.75;MQ0=1;MQRankSum=-0.159;QD=5.89;ReadPosRankSum=0.619;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,9:38:99:252,0,952
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|
|
3805 chr1 145416 . T C 1041.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=23.0537;MLEAC=2;MLEAF=1.00;MQ=54.28;MQ0=1;QD=31.57;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,33:33:87:1070,87,0
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|
|
3806 chr1 145429 . C T 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=33;Dels=0.00;FS=4.709;HaplotypeScore=14.4456;MLEAC=1;MLEAF=0.500;MQ=53.98;MQ0=1;MQRankSum=-2.077;QD=14.17;ReadPosRankSum=1.057;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:496,0,578
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|
|
3807 chr1 145442 . C T 489.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.854;DP=28;Dels=0.00;FS=4.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.85;MQ0=1;MQRankSum=2.415;QD=17.49;ReadPosRankSum=-2.025;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,16:28:99:518,0,409
|
|
|
3808 chr1 145448 . T C 377.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.88;MQ0=0;QD=31.09;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:406,30,0
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|
|
3809 chr1 145453 . A G 385.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.88;MQ0=0;QD=26.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:414,30,0
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|
|
3810 chr1 145503 . G A,C 789.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.79;MQ0=0;QD=29.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,19,8:27:99:956,264,207,691,0,667
|
|
|
3811 chr1 145509 . G A 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=26;Dels=0.00;FS=1.970;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=0.472;QD=23.26;ReadPosRankSum=1.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,18:26:99:633,0,240
|
|
|
3812 chr1 145512 . C T 213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.259;DP=23;Dels=0.00;FS=1.824;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=1.711;QD=9.29;ReadPosRankSum=-1.840;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:242,0,524
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|
|
3813 chr1 145513 . G A 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.226;DP=23;Dels=0.00;FS=1.824;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-1.904;QD=20.90;ReadPosRankSum=1.646;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:509,0,246
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|
|
3814 chr1 145515 . G A 222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.013;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=1.126;QD=10.13;ReadPosRankSum=-1.945;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,8:22:99:251,0,503
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|
|
3815 chr1 145531 . A G 307.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.177;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=-1.288;QD=17.10;ReadPosRankSum=-1.733;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,10:18:99:336,0,240
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|
|
3816 chr1 145534 . C T 216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.280;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=2.518;QD=11.41;ReadPosRankSum=2.106;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:11,8:19:99:245,0,339
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|
|
3817 chr1 145538 . T C 270.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.376;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-1.376;QD=16.92;ReadPosRankSum=-2.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,9:16:99:299,0,219
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|
|
3818 chr1 145544 . T C 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.000;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.50;MQ0=0;MQRankSum=1.134;QD=11.81;ReadPosRankSum=2.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,5:12:99:170,0,230
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|
|
3819 chr1 145555 . A G 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.851;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=-0.470;QD=12.78;ReadPosRankSum=-2.450;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:5,5:10:99:156,0,173
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|
|
3820 chr1 145615 . A C 535.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=1.9330;MLEAC=2;MLEAF=1.00;MQ=55.87;MQ0=0;QD=32.10;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:564,42,0
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|
3821 chr1 145642 . A G 1135.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=8.6529;MLEAC=2;MLEAF=1.00;MQ=54.53;MQ0=0;QD=31.83;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1164,87,0
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|
|
3822 chr1 145654 . T C 490.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=31;Dels=0.00;FS=1.862;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.94;MQ0=1;MQRankSum=-2.198;QD=15.83;ReadPosRankSum=0.249;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,15:31:99:519,0,451
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|
3823 chr1 145666 . G A 452.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.376;DP=33;Dels=0.00;FS=1.845;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.78;MQ0=2;MQRankSum=-1.364;QD=13.72;ReadPosRankSum=1.482;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:481,0,521
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|
|
3824 chr1 145673 . T C 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.099;DP=35;Dels=0.00;FS=1.624;HaplotypeScore=15.4641;MLEAC=1;MLEAF=0.500;MQ=52.28;MQ0=2;MQRankSum=0.955;QD=13.76;ReadPosRankSum=-0.630;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:510,0,570
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|
3825 chr1 145676 . A G 468.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.570;DP=36;Dels=0.00;FS=1.666;HaplotypeScore=16.4306;MLEAC=1;MLEAF=0.500;MQ=52.51;MQ0=2;MQRankSum=0.707;QD=13.02;ReadPosRankSum=0.224;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,18:36:99:497,0,607
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|
|
3826 chr1 145688 . A G 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.302;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=2;MQRankSum=-0.944;QD=15.17;ReadPosRankSum=-0.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:544,0,419
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|
|
3827 chr1 145689 . C T 396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=2;MQRankSum=1.171;QD=11.67;ReadPosRankSum=0.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:425,0,541
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|
|
3828 chr1 145706 . C T 986.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=2;QD=32.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,30:30:78:1015,78,0
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|
|
3829 chr1 145712 . A G 1007.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.65;MQ0=2;QD=32.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,31:31:81:1036,81,0
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|
|
3830 chr1 145783 . G A 363.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.564;DP=19;Dels=0.00;FS=2.199;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.549;QD=19.15;ReadPosRankSum=2.409;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,12:19:99:392,0,216
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|
|
3831 chr1 145845 . C T 1598.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.27;MQ0=0;QD=26.69;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1627,120,0
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|
|
3832 chr1 145926 . A T 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.984;DP=43;Dels=0.00;FS=1.186;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=2.423;QD=15.23;ReadPosRankSum=0.621;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:683,0,719
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|
|
3833 chr1 145928 . A T 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.484;DP=41;Dels=0.00;FS=2.731;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.19;MQ0=0;MQRankSum=-0.745;QD=16.12;ReadPosRankSum=-0.588;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:689,0,634
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|
|
3834 chr1 145949 . T C 762.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.879;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-1.907;QD=16.95;ReadPosRankSum=0.971;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:791,0,650
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|
|
3835 chr1 145950 . G C 1750.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.62;MQ0=0;QD=26.60;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1779,135,0
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|
|
3836 chr1 145957 . T C 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.38;MQ0=0;MQRankSum=-2.937;QD=19.86;ReadPosRankSum=0.461;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,28:46:99:942,0,588
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|
|
3837 chr1 145961 . G A 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.485;DP=47;Dels=0.00;FS=1.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.44;MQ0=0;MQRankSum=-3.067;QD=19.74;ReadPosRankSum=1.160;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,28:47:99:956,0,621
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|
|
3838 chr1 145971 . T C 1794.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.38;MQ0=0;QD=30.91;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1823,135,0
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|
|
3839 chr1 145982 . C T 1821.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.7334;MLEAC=2;MLEAF=1.00;MQ=57.44;MQ0=0;QD=35.83;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1850,138,0
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|
|
3840 chr1 145991 . T C 1257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.420;DP=40;Dels=0.00;FS=2.157;HaplotypeScore=1.7334;MLEAC=1;MLEAF=0.500;MQ=57.75;MQ0=0;MQRankSum=-0.969;QD=31.44;ReadPosRankSum=2.998;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:4,36:40:39:1286,0,39
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|
|
3841 chr1 145995 . C T 1327.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.079;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=2.3985;MLEAC=2;MLEAF=1.00;MQ=57.63;MQ0=0;MQRankSum=-0.621;QD=34.94;ReadPosRankSum=2.190;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:2,36:38:38:1356,38,0
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|
|
3842 chr1 146000 . G A 1358.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.66;MQ0=0;QD=22.90;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1387,108,0
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|
|
3843 chr1 146028 . T C 1707.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.8730;MLEAC=2;MLEAF=1.00;MQ=58.54;MQ0=0;QD=27.76;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1736,135,0
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|
|
3844 chr1 146053 . A G 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.384;DP=42;Dels=0.00;FS=1.216;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.654;QD=14.85;ReadPosRankSum=-1.484;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:652,0,659
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|
|
3845 chr1 146141 . G C 886.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.446;DP=55;Dels=0.00;FS=1.026;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.379;QD=16.12;ReadPosRankSum=0.093;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:915,0,948
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|
|
3846 chr1 146183 . C T 898.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.673;DP=61;Dels=0.00;FS=13.794;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=0.166;QD=14.73;ReadPosRankSum=1.165;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,28:61:99:927,0,1096
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|
|
3847 chr1 146259 . G A 679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.772;DP=50;Dels=0.00;FS=1.112;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-2.160;QD=13.60;ReadPosRankSum=0.225;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:708,0,962
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|
|
3848 chr1 146273 . A G 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.267;DP=47;Dels=0.00;FS=2.512;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=-0.672;QD=14.27;ReadPosRankSum=0.117;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:699,0,859
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|
|
3849 chr1 146296 . T C 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.123;DP=51;Dels=0.00;FS=2.461;HaplotypeScore=1.7074;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-1.406;QD=13.64;ReadPosRankSum=0.802;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:724,0,886
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|
|
3850 chr1 146334 . G A 730.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.744;DP=54;Dels=0.00;FS=15.099;HaplotypeScore=4.3788;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=0.234;QD=13.53;ReadPosRankSum=-0.892;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,28:54:99:759,0,888
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|
|
3851 chr1 146352 . A C 847.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.498;DP=51;Dels=0.00;FS=10.821;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=1.008;QD=16.62;ReadPosRankSum=0.801;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:876,0,875
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|
|
3852 chr1 146412 . A G 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.096;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-1.487;QD=17.29;ReadPosRankSum=-0.974;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:841,0,718
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|
|
3853 chr1 146446 . G T 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.410;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=57.03;MQ0=0;MQRankSum=-3.670;QD=13.83;ReadPosRankSum=-0.730;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:706,0,869
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|
|
3854 chr1 146451 . T C 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.785;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=56.97;MQ0=0;MQRankSum=-1.455;QD=13.94;ReadPosRankSum=-0.796;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:725,0,868
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|
|
3855 chr1 146456 . G C 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.673;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=3.9978;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=0;MQRankSum=-3.167;QD=10.90;ReadPosRankSum=0.452;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,19:44:99:508,0,846
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|
|
3856 chr1 146467 . C T 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.106;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=55.70;MQ0=0;MQRankSum=-3.722;QD=12.56;ReadPosRankSum=-0.562;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:493,0,671
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|
|
3857 chr1 146489 . T A 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.236;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=6.7989;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=-3.721;QD=8.78;ReadPosRankSum=3.030;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,12:38:99:362,0,945
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|
|
3858 chr1 146502 . C T 460.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.559;DP=40;Dels=0.00;FS=2.861;HaplotypeScore=82.1865;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=0;MQRankSum=-2.486;QD=11.52;ReadPosRankSum=2.989;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:489,0,888
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|
|
3859 chr1 146626 . C A 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.124;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=0.151;QD=9.56;ReadPosRankSum=-0.179;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,14:41:99:420,0,892
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|
|
3860 chr1 146707 . A T 748.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.116;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=51.1918;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-0.045;QD=14.13;ReadPosRankSum=-0.846;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:777,0,951
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|
|
3861 chr1 146722 . C T 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.569;DP=53;Dels=0.00;FS=2.427;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-0.514;QD=12.00;ReadPosRankSum=0.966;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:664,0,1073
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|
3862 chr1 146734 . G A 460.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.160;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-2.057;QD=8.69;ReadPosRankSum=2.226;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:489,0,1193
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|
|
3863 chr1 146736 . C T 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.042;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-1.906;QD=9.05;ReadPosRankSum=2.432;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:508,0,1187
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|
|
3864 chr1 146737 . T C 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.399;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-2.038;QD=9.15;ReadPosRankSum=2.507;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:513,0,1186
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|
|
3865 chr1 146738 . G A 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.178;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-1.005;QD=8.94;ReadPosRankSum=2.470;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:502,0,1205
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|
|
3866 chr1 146751 . T C 1086.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.546;DP=56;Dels=0.00;FS=8.313;HaplotypeScore=2.7878;MLEAC=1;MLEAF=0.500;MQ=57.36;MQ0=1;MQRankSum=2.036;QD=19.41;ReadPosRankSum=-0.424;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,34:56:99:1115,0,613
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|
|
3867 chr1 146757 . T C 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.536;DP=54;Dels=0.00;FS=8.599;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=57.26;MQ0=1;MQRankSum=-1.537;QD=11.00;ReadPosRankSum=-0.118;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:622,0,1058
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|
|
3868 chr1 146765 . T C 455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.851;DP=50;Dels=0.00;FS=2.814;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=57.67;MQ0=1;MQRankSum=-1.838;QD=9.12;ReadPosRankSum=0.011;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,18:50:99:484,0,1120
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|
|
3869 chr1 146805 . C G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.862;DP=39;Dels=0.00;FS=3.130;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=1;MQRankSum=0.738;QD=8.51;ReadPosRankSum=0.585;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:360,0,832
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|
|
3870 chr1 146811 . A T 447.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.860;DP=41;Dels=0.00;FS=1.258;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=1;MQRankSum=-0.246;QD=10.92;ReadPosRankSum=-0.821;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:476,0,771
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|
|
3871 chr1 146917 . T C 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.342;DP=34;Dels=0.00;FS=11.504;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-0.919;QD=22.14;ReadPosRankSum=0.523;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,22:34:99:781,0,382
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|
|
3872 chr1 146962 . C T 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.455;DP=33;Dels=0.00;FS=8.473;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.13;MQ0=0;MQRankSum=0.387;QD=12.14;ReadPosRankSum=-0.387;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,13:33:99:429,0,656
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|
|
3873 chr1 147004 . A G 326.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.46;MQ0=0;QD=28.95;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,9:9:27:355,27,0
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|
|
3874 chr1 147012 . A G 322.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.46;MQ0=0;QD=27.55;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,9:9:27:351,27,0
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|
|
3875 chr1 147033 . A G 283.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.29;MQ0=0;QD=27.26;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:312,24,0
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|
|
3876 chr1 147043 . G A 158.9 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.198;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.14;MQ0=1;MQRankSum=1.495;QD=19.86;ReadPosRankSum=0.922;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:3,5:8:15:187,15,0
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|
|
3877 chr1 147044 . C T 132.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.720;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.27;MQ0=1;MQRankSum=1.380;QD=18.86;ReadPosRankSum=1.380;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:3,4:7:12:160,12,0
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|
|
3878 chr1 147046 . C T 132.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.638;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.75;MQ0=1;MQRankSum=2.017;QD=14.67;ReadPosRankSum=2.017;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:5,4:9:12:160,12,0
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|
|
3879 chr1 147053 . C T 129.03 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.51;MQ0=1;QD=11.73;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,11:11:12:157,12,0
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|
|
3880 chr1 147055 . T C 126.03 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.51;MQ0=1;QD=11.46;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,11:11:12:154,12,0
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|
|
3881 chr1 147074 . G A 120.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.659;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=4.7802;MLEAC=1;MLEAF=0.500;MQ=29.47;MQ0=1;MQRankSum=2.617;QD=5.25;ReadPosRankSum=-1.880;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,6:23:99:149,0,214
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|
|
3882 chr1 147113 . A C 82.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=27.3842;MLEAC=1;MLEAF=0.500;MQ=25.38;MQ0=3;MQRankSum=1.937;QD=2.30;ReadPosRankSum=2.310;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,6:36:99:111,0,296
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|
|
3883 chr1 147139 . G A 323.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.091;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=16.6145;MLEAC=1;MLEAF=0.500;MQ=25.38;MQ0=11;MQRankSum=2.940;QD=6.11;ReadPosRankSum=1.127;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,18:53:99:352,0,249
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|
|
3884 chr1 147150 . T G 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.178;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=10.0978;MLEAC=1;MLEAF=0.500;MQ=26.62;MQ0=11;MQRankSum=-1.429;QD=2.04;ReadPosRankSum=-1.554;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:128,0,456
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|
|
3885 chr1 147170 . G A 326.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.347;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=42.8592;MLEAC=1;MLEAF=0.500;MQ=26.42;MQ0=13;MQRankSum=3.898;QD=6.95;ReadPosRankSum=-1.311;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,13:47:99:355,0,181
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|
|
3886 chr1 147223 . T C 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.307;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=4.9798;MLEAC=1;MLEAF=0.500;MQ=20.60;MQ0=4;MQRankSum=-2.013;QD=3.22;ReadPosRankSum=-1.604;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,18:26:99:112,0,126
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|
|
3887 chr1 147226 . G C 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.109;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=4.9798;MLEAC=1;MLEAF=0.500;MQ=21.38;MQ0=3;MQRankSum=1.702;QD=2.41;ReadPosRankSum=1.702;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,8:24:86:86,0,115
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|
|
3888 chr1 147227 . C A 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.182;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=6.9023;MLEAC=1;MLEAF=0.500;MQ=21.38;MQ0=3;MQRankSum=0.910;QD=0.99;ReadPosRankSum=-0.667;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,5:24:52:52,0,159
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|
|
3889 chr1 147238 . A G 178.8 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=5.5670;MLEAC=2;MLEAF=1.00;MQ=23.04;MQ0=2;QD=10.52;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,17:17:21:207,21,0
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|
3890 chr1 147243 . C T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=7.5617;MLEAC=1;MLEAF=0.500;MQ=22.90;MQ0=2;MQRankSum=0.755;QD=3.39;ReadPosRankSum=1.200;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,8:20:96:96,0,131
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|
3891 chr1 147246 . A T 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.236;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=7.5617;MLEAC=1;MLEAF=0.500;MQ=24.50;MQ0=1;MQRankSum=1.559;QD=2.56;ReadPosRankSum=-2.126;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,4:21:82:82,0,176
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|
3892 chr1 147259 . A G 289.56 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.540;DP=19;Dels=0.00;FS=4.393;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.17;MQ0=1;MQRankSum=1.185;QD=15.24;ReadPosRankSum=-1.303;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:3,16:19:7:317,7,0
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|
3893 chr1 147272 . C T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.709;DP=16;Dels=0.00;FS=3.522;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=31.58;MQ0=1;MQRankSum=2.298;QD=9.11;ReadPosRankSum=-2.062;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,6:16:99:174,0,100
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|
3894 chr1 147273 . T C 302.78 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=31.58;MQ0=1;QD=18.92;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,15:16:27:331,27,0
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|
|
3895 chr1 147296 . A G 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.795;DP=18;Dels=0.00;FS=7.404;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.13;MQ0=0;MQRankSum=3.532;QD=16.93;ReadPosRankSum=-0.530;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,9:18:51:333,0,51
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|
3896 chr1 147357 . A T 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.153;DP=30;Dels=0.00;FS=28.709;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.13;MQ0=6;MQRankSum=-3.766;QD=4.79;ReadPosRankSum=-1.133;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,14:30:99:172,0,529
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|
3897 chr1 147416 . T C 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.937;DP=10;Dels=0.00;FS=15.441;HaplotypeScore=26.0957;MLEAC=1;MLEAF=0.500;MQ=30.35;MQ0=3;MQRankSum=-1.754;QD=3.98;ReadPosRankSum=-1.754;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,4:10:68:68,0,134
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|
3898 chr1 147424 . A G 110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.380;DP=8;Dels=0.00;FS=11.761;HaplotypeScore=2.8995;MLEAC=1;MLEAF=0.500;MQ=30.85;MQ0=2;MQRankSum=1.380;QD=13.85;ReadPosRankSum=1.380;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:4,4:8:31:139,0,31
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|
3899 chr1 147427 . T C 164.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.98;MQ0=1;QD=23.55;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:193,18,0
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|
3900 chr1 147428 . T C 173.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.98;MQ0=1;QD=24.83;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:202,18,0
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|
3901 chr1 147440 . C T 145.96 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.219;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=30.86;MQ0=2;MQRankSum=2.219;QD=13.27;ReadPosRankSum=-0.876;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,5:11:5:173,0,5
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|
3902 chr1 147461 . G A 174.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.074;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=8.9694;MLEAC=1;MLEAF=0.500;MQ=32.41;MQ0=2;MQRankSum=3.016;QD=11.65;ReadPosRankSum=-1.493;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,6:15:24:203,0,24
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|
3903 chr1 147474 . C T 286.9 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.223;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=10.9207;MLEAC=1;MLEAF=0.500;MQ=41.09;MQ0=2;MQRankSum=3.281;QD=15.94;ReadPosRankSum=-2.752;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,9:18:15:315,0,15
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|
3904 chr1 147490 . G A 297.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.899;DP=23;Dels=0.00;FS=3.834;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.48;MQ0=0;MQRankSum=2.760;QD=12.95;ReadPosRankSum=3.318;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:326,0,430
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|
|
3905 chr1 147522 . C T 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.004;DP=30;Dels=0.00;FS=1.449;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=54.65;MQ0=0;MQRankSum=-3.516;QD=17.83;ReadPosRankSum=-0.963;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:563,0,394
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|
|
3906 chr1 147528 . A G 1043.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.18;MQ0=0;QD=31.37;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1072,81,0
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|
|
3907 chr1 147529 . T C 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.492;DP=27;Dels=0.00;FS=1.598;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.18;MQ0=0;MQRankSum=3.380;QD=12.77;ReadPosRankSum=0.962;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,11:27:99:373,0,495
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|
|
3908 chr1 147542 . C T 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.567;DP=33;Dels=0.00;FS=5.188;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.17;MQ0=0;MQRankSum=-2.900;QD=17.30;ReadPosRankSum=-0.234;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,17:33:99:599,0,528
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|
|
3909 chr1 147543 . C T 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=34;Dels=0.00;FS=3.064;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.26;MQ0=0;MQRankSum=-1.639;QD=17.52;ReadPosRankSum=-0.535;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:624,0,489
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|
|
3910 chr1 147546 . G A 434.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.043;DP=35;Dels=0.00;FS=3.108;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=3.560;QD=12.42;ReadPosRankSum=0.248;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:463,0,624
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|
|
3911 chr1 147575 . G A 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.453;DP=42;Dels=0.00;FS=4.613;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.79;MQ0=0;MQRankSum=-2.836;QD=20.26;ReadPosRankSum=-0.194;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,26:42:99:879,0,470
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|
|
3912 chr1 147578 . A C 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.122;DP=41;Dels=0.00;FS=2.845;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.07;MQ0=0;MQRankSum=2.964;QD=10.43;ReadPosRankSum=0.744;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:456,0,851
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|
|
3913 chr1 147586 . C T 1415.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=53.48;MQ0=0;QD=32.80;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1444,114,0
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|
|
3914 chr1 147591 . C T 640.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=35;Dels=0.00;FS=1.344;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-2.317;QD=18.31;ReadPosRankSum=0.850;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:669,0,479
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|
|
3915 chr1 147594 . G C,T 1053.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1,1;MLEAF=0.500,0.500;MQ=53.02;MQ0=0;QD=30.98;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,19,15:34:99:1240,557,500,683,0,638
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|
|
3916 chr1 147597 . A G 1257.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.7338;MLEAC=2;MLEAF=1.00;MQ=52.79;MQ0=0;QD=24.91;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1286,99,0
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|
|
3917 chr1 147598 . G A 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.387;DP=33;Dels=0.00;FS=5.093;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=52.79;MQ0=0;MQRankSum=-2.045;QD=19.33;ReadPosRankSum=0.166;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,20:33:99:666,0,407
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|
|
3918 chr1 147606 . A C 1323.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=52.20;MQ0=0;QD=29.38;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1352,105,0
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|
|
3919 chr1 147628 . C T 1132.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.90;MQ0=0;QD=33.91;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1161,90,0
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|
|
3920 chr1 147635 . A G 947.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.40;MQ0=0;QD=28.17;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:976,78,0
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|
|
3921 chr1 147636 . C T 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.792;DP=26;Dels=0.00;FS=1.796;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.40;MQ0=0;MQRankSum=-2.081;QD=23.18;ReadPosRankSum=1.272;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,19:26:99:631,0,203
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|
3922 chr1 147641 . T A 609.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.241;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=0;MQRankSum=-1.623;QD=24.39;ReadPosRankSum=1.241;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,19:25:99:638,0,170
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|
|
3923 chr1 147653 . T G 1125.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.44;MQ0=0;QD=36.65;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1154,93,0
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|
|
3924 chr1 147665 . C T 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.781;DP=31;Dels=0.00;FS=11.051;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.68;MQ0=0;MQRankSum=2.182;QD=11.86;ReadPosRankSum=-1.741;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,13:31:99:396,0,590
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|
3925 chr1 147671 . C T 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=30;Dels=0.00;FS=8.496;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=-1.517;QD=15.93;ReadPosRankSum=2.099;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,16:30:99:506,0,416
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|
3926 chr1 147698 . T C 448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.327;DP=29;Dels=0.00;FS=11.831;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=-0.240;QD=15.47;ReadPosRankSum=-2.160;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,14:29:99:477,0,517
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|
3927 chr1 147700 . A G 1091.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=2.4530;MLEAC=2;MLEAF=1.00;MQ=58.55;MQ0=0;QD=32.47;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1120,84,0
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|
3928 chr1 147730 . T C 494.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.074;DP=38;Dels=0.00;FS=24.449;HaplotypeScore=2.5770;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=1.345;QD=13.02;ReadPosRankSum=1.109;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:523,0,753
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|
3929 chr1 147779 . C T 1482.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.43;MQ0=0;QD=28.95;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1511,111,0
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|
3930 chr1 147815 . G A 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.116;DP=38;Dels=0.00;FS=5.625;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.779;QD=10.52;ReadPosRankSum=1.129;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S6N|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,13:38:99:428,0,860
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3931 chr1 147816 . C T 396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.538;DP=38;Dels=0.00;FS=5.221;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.154;QD=10.44;ReadPosRankSum=1.292;EFF=SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S6|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,13:38:99:425,0,850
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3932 chr1 147861 . G A 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.261;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-2.322;QD=18.06;ReadPosRankSum=-0.782;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S21|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:823,0,602
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3933 chr1 147863 . G C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.355;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-1.540;QD=18.84;ReadPosRankSum=-0.782;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aCc|S22T|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:857,0,597
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3934 chr1 147893 . A C 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=28;Dels=0.00;FS=12.411;HaplotypeScore=17.4716;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.534;QD=13.31;ReadPosRankSum=1.694;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tCt|Y32S|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:401,0,517
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3935 chr1 147940 . G A 136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.992;DP=60;Dels=0.00;FS=5.651;HaplotypeScore=4.9890;MLEAC=1;MLEAF=0.500;MQ=51.15;MQ0=1;MQRankSum=2.013;QD=2.28;ReadPosRankSum=0.601;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E48K|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:51,9:60:99:165,0,1548
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3936 chr1 147974 . G T 2172.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=52.02;MQ0=1;QD=32.90;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tTg|W59L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2201,172,0
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3937 chr1 147980 . T C 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.561;DP=60;Dels=0.00;FS=2.594;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=53.04;MQ0=1;MQRankSum=-5.013;QD=5.68;ReadPosRankSum=2.921;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L61S|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:42,18:60:99:369,0,1413
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3938 chr1 148008 . T G 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.047;DP=70;Dels=0.00;FS=5.868;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-4.821;QD=6.14;ReadPosRankSum=0.000;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T70|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:51,19:70:99:458,0,1746
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3939 chr1 148023 . G A 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.485;DP=65;Dels=0.00;FS=8.565;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=-4.083;QD=6.41;ReadPosRankSum=0.082;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V75|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:445,0,1615
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3940 chr1 148028 . C T 325.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.066;DP=60;Dels=0.00;FS=14.560;HaplotypeScore=3.3988;MLEAC=1;MLEAF=0.500;MQ=58.07;MQ0=0;MQRankSum=-4.165;QD=5.43;ReadPosRankSum=0.768;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S77L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:45,15:60:99:354,0,1522
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3941 chr1 148029 . G A 296.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.097;DP=57;Dels=0.00;FS=9.963;HaplotypeScore=3.3988;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=0;MQRankSum=-2.445;QD=5.21;ReadPosRankSum=1.708;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S77|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:43,13:57:99:325,0,1421
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3942 chr1 148050 . T C 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=0;MQRankSum=2.073;QD=10.00;ReadPosRankSum=-0.265;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I84|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:41,24:65:99:678,0,1415
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3943 chr1 148062 . G A 2262.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=1.3990;MLEAC=2;MLEAF=1.00;MQ=58.19;MQ0=0;QD=26.81;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R88|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2291,178,0
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3944 chr1 148077 . T G 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.434;DP=53;Dels=0.00;FS=12.734;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=0;MQRankSum=-4.267;QD=7.07;ReadPosRankSum=0.313;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H93Q|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:39,14:53:99:403,0,1389
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|
3945 chr1 148078 . C A 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.438;DP=54;Dels=0.00;FS=12.716;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=0;MQRankSum=-4.017;QD=6.61;ReadPosRankSum=0.365;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P94T|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:40,14:54:99:385,0,1444
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|
3946 chr1 148095 . C T 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.542;DP=44;Dels=0.00;FS=14.379;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=-3.117;QD=6.61;ReadPosRankSum=1.003;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A99|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:33,11:44:99:319,0,1163
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|
|
3947 chr1 148104 . C T 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.046;DP=48;Dels=0.00;FS=16.904;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.38;MQ0=0;MQRankSum=-4.176;QD=7.10;ReadPosRankSum=-0.348;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A102|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:35,13:48:99:369,0,1201
|
|
|
3948 chr1 148117 . T C 207.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.521;DP=50;Dels=0.00;FS=18.397;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=0;MQRankSum=-3.965;QD=4.16;ReadPosRankSum=1.152;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S107P|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:40,10:50:99:236,0,1399
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|
|
3949 chr1 148124 . C T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.360;DP=49;Dels=0.00;FS=20.451;HaplotypeScore=1.8499;MLEAC=1;MLEAF=0.500;MQ=57.15;MQ0=0;MQRankSum=-4.155;QD=3.73;ReadPosRankSum=0.409;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T109I|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:39,10:49:99:211,0,1394
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|
|
3950 chr1 148128 . T C 178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.819;DP=48;Dels=0.00;FS=20.451;HaplotypeScore=45.3427;MLEAC=1;MLEAF=0.500;MQ=56.97;MQ0=0;MQRankSum=-4.649;QD=3.72;ReadPosRankSum=0.608;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A110|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:39,9:48:99:207,0,1389
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|
|
3951 chr1 148133 . A G 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.055;DP=46;Dels=0.00;FS=20.653;HaplotypeScore=118.8295;MLEAC=1;MLEAF=0.500;MQ=56.83;MQ0=0;MQRankSum=-4.624;QD=3.82;ReadPosRankSum=-0.194;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D112G|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:37,9:46:99:204,0,1210
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|
|
3952 chr1 148165 . C G 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=43;Dels=0.00;FS=1.213;HaplotypeScore=4.9810;MLEAC=1;MLEAF=0.500;MQ=56.32;MQ0=0;MQRankSum=1.859;QD=11.99;ReadPosRankSum=-1.096;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Gcc|P123A|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:544,0,806
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|
|
3953 chr1 148184 . A G 1381.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=2.9827;MLEAC=2;MLEAF=1.00;MQ=56.12;MQ0=0;QD=29.22;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K129R|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1410,111,0
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|
|
3954 chr1 148218 . T A 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.156;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.57;MQ0=0;MQRankSum=0.826;QD=13.38;ReadPosRankSum=0.216;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcA|S140|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:590,0,747
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|
|
3955 chr1 148366 . C G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.171;DP=46;Dels=0.00;FS=2.594;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=1;MQRankSum=0.742;QD=18.06;ReadPosRankSum=0.811;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:859,0,635
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|
|
3956 chr1 148435 . A C 1097.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.646;DP=54;Dels=0.00;FS=9.969;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=0.801;QD=20.33;ReadPosRankSum=-0.361;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,32:54:99:1126,0,692
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|
|
3957 chr1 148463 . A G 1201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.268;DP=54;Dels=0.00;FS=1.155;HaplotypeScore=28.9952;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-0.199;QD=22.25;ReadPosRankSum=0.507;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,35:54:99:1230,0,586
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|
|
3958 chr1 148468 . A G 1266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.651;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=15.2316;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.761;QD=23.46;ReadPosRankSum=0.615;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:18,36:54:99:1295,0,544
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|
|
3959 chr1 148595 . C T 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.094;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=1.341;QD=12.88;ReadPosRankSum=-0.048;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:685,0,1002
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|
|
3960 chr1 148617 . G A 749.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.242;DP=50;Dels=0.00;FS=1.142;HaplotypeScore=2.7334;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=1.203;QD=15.00;ReadPosRankSum=-1.901;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:778,0,841
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|
|
3961 chr1 148704 . G C 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=51;Dels=0.00;FS=3.975;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=0.330;QD=17.33;ReadPosRankSum=-0.481;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:912,0,798
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|
|
3962 chr1 148761 . A T 1165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.413;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=0.244;QD=17.66;ReadPosRankSum=0.925;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1194,0,997
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|
|
3963 chr1 148794 . T C 1570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.757;DP=84;Dels=0.00;FS=0.829;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-0.198;QD=18.70;ReadPosRankSum=-0.117;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:37,47:84:99:1599,0,1205
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|
|
3964 chr1 148795 . C T 1196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.725;DP=81;Dels=0.00;FS=0.833;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.043;QD=14.77;ReadPosRankSum=-0.327;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:44,37:81:99:1225,0,1499
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|
|
3965 chr1 148840 . T A 1013.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.283;DP=67;Dels=0.00;FS=6.538;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.018;QD=15.13;ReadPosRankSum=0.094;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:36,31:67:99:1042,0,1215
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|
|
3966 chr1 148975 . A T 1278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.432;DP=70;Dels=0.00;FS=2.050;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.56;MQ0=0;MQRankSum=-2.446;QD=18.27;ReadPosRankSum=-0.383;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:32,38:70:99:1307,0,1024
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|
3967 chr1 148997 . T C 2678.77 . AC=2;AF=1.00;AN=2;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.02;MQ0=0;QD=25.77;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,68:68:99:2707,205,0
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|
|
3968 chr1 149029 . T C 1230.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.008;DP=64;Dels=0.00;FS=7.922;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=4;MQRankSum=-3.991;QD=19.23;ReadPosRankSum=0.098;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,40:64:99:1259,0,799
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|
|
3969 chr1 149049 . C T 841.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.530;DP=53;Dels=0.00;FS=4.125;HaplotypeScore=3.9326;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=4;MQRankSum=-3.050;QD=15.88;ReadPosRankSum=0.650;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:870,0,827
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|
|
3970 chr1 149054 . T A 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.693;DP=53;Dels=0.00;FS=1.097;HaplotypeScore=2.9329;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=4;MQRankSum=-3.556;QD=14.32;ReadPosRankSum=1.012;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:787,0,898
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|
|
3971 chr1 149065 . C T 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.127;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=47.38;MQ0=4;MQRankSum=3.705;QD=16.74;ReadPosRankSum=-1.056;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:748,0,583
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|
|
3972 chr1 149079 . T A 1585.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.50;MQ0=0;QD=35.89;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1614,120,0
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|
|
3973 chr1 149083 . G A 607.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.106;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.98;MQ0=0;MQRankSum=1.535;QD=16.43;ReadPosRankSum=1.595;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:18,19:37:99:636,0,597
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|
|
3974 chr1 149099 . C T 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.884;DP=40;Dels=0.00;FS=2.794;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-0.095;QD=14.47;ReadPosRankSum=-0.340;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,18:40:99:607,0,754
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|
|
3975 chr1 149136 . A C 1526.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.87;MQ0=0;QD=32.84;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1555,117,0
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|
|
3976 chr1 149156 . G A 46.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.214;DP=52;Dels=0.00;FS=6.760;HaplotypeScore=3.3564;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.965;QD=0.90;ReadPosRankSum=-3.566;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R158|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:45,7:52:75:75,0,1569
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|
|
3977 chr1 149170 . A G 20.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.215;DP=58;Dels=0.00;FS=6.984;HaplotypeScore=11.3843;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-0.167;QD=0.36;ReadPosRankSum=-0.215;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E163G|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:51,7:58:49:49,0,1750
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|
|
3978 chr1 149174 . A G 793.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.409;DP=60;Dels=0.00;FS=14.447;HaplotypeScore=10.5956;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=0.030;QD=13.23;ReadPosRankSum=0.195;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P164|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:35,25:60:99:822,0,1037
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|
|
3979 chr1 149224 . T C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.926;DP=47;Dels=0.00;FS=19.146;HaplotypeScore=12.8749;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=1.421;QD=14.51;ReadPosRankSum=-0.769;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I181T|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:20,21:47:99:710,0,673
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|
|
3980 chr1 149225 . C G 72.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.685;DP=47;Dels=0.00;FS=6.565;HaplotypeScore=12.8749;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.526;QD=1.55;ReadPosRankSum=1.164;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atC/atG|I181M|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:41,6:47:99:101,0,1493
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|
|
3981 chr1 149237 . G A 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.474;DP=43;Dels=0.00;FS=4.406;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=0.284;QD=0.81;ReadPosRankSum=1.118;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L185|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:38,5:43:63:63,0,1390
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|
|
3982 chr1 149253 . C T 1318.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.87;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P191S|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1347,105,0
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|
|
3983 chr1 149279 . G A 504.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.121;DP=34;Dels=0.00;FS=8.198;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.052;QD=14.85;ReadPosRankSum=0.155;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S199|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:18,16:34:99:533,0,627
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|
|
3984 chr1 149379 . T C 993.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.329;DP=49;Dels=0.00;FS=1.117;HaplotypeScore=2.8936;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.187;QD=20.28;ReadPosRankSum=0.193;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:20,29:49:99:1022,0,551
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3985 chr1 149421 . T C 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.477;DP=43;Dels=0.00;FS=1.218;HaplotypeScore=3.8299;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.086;QD=13.09;ReadPosRankSum=0.037;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,19:43:99:591,0,836
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|
3986 chr1 149472 . A G 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.173;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.074;QD=12.76;ReadPosRankSum=-0.015;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:513,0,690
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|
3987 chr1 149514 . C T 435.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.438;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.243;QD=12.10;ReadPosRankSum=1.444;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:464,0,734
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|
3988 chr1 149653 . G T 579.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.40;MQ0=1;QD=28.93;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,16:16:45:608,45,0
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|
|
3989 chr1 149713 . T G 538.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.394;DP=42;Dels=0.00;FS=1.480;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.750;QD=12.83;ReadPosRankSum=0.496;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:567,0,822
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|
3990 chr1 149716 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.591;DP=44;Dels=0.00;FS=3.214;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=-0.177;QD=14.22;ReadPosRankSum=-0.365;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:654,0,836
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|
3991 chr1 149737 . A G 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.238;QD=16.15;ReadPosRankSum=1.192;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:755,0,792
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|
3992 chr1 149745 . C T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.331;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.697;QD=13.88;ReadPosRankSum=1.519;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:653,0,850
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|
3993 chr1 149746 . A G 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.247;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.420;QD=13.21;ReadPosRankSum=1.732;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:649,0,910
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3994 chr1 149780 . T C 390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.077;DP=33;Dels=0.00;FS=3.967;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.998;QD=11.84;ReadPosRankSum=-1.803;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,13:33:99:419,0,669
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3995 chr1 149946 . T C 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.827;DP=53;Dels=0.00;FS=1.147;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=-1.482;QD=12.69;ReadPosRankSum=0.409;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,21:53:99:701,0,1128
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3996 chr1 149947 . G A 2084.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=59.80;MQ0=0;QD=27.53;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2113,157,0
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|
3997 chr1 149959 . T G 1968.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.79;MQ0=0;QD=31.52;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1997,150,0
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3998 chr1 149962 . T C 506.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=50;Dels=0.00;FS=1.172;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.553;QD=10.14;ReadPosRankSum=-0.471;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:535,0,1193
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|
3999 chr1 150069 . A G 699.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.948;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=-1.083;QD=17.49;ReadPosRankSum=0.217;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I248V|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_150006_150117) GT:AD:DP:GQ:PL 0/1:19,21:40:99:728,0,642
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|
4000 chr1 150083 . G A 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.606;DP=42;Dels=0.00;FS=2.885;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=2.679;QD=14.76;ReadPosRankSum=0.859;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V252|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_150006_150117) GT:AD:DP:GQ:PL 0/1:23,19:42:99:648,0,802
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4001 chr1 150232 . C T 2061.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=59.55;MQ0=0;QD=24.48;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2090,159,0
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|
4002 chr1 150236 . G A 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.696;DP=55;Dels=0.00;FS=5.672;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.713;QD=12.12;ReadPosRankSum=0.850;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:695,0,1131
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4003 chr1 150249 . C G 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.775;DP=55;Dels=0.00;FS=3.715;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.844;QD=13.76;ReadPosRankSum=2.150;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,24:55:99:785,0,958
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4004 chr1 150265 . C T 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.317;DP=57;Dels=0.00;FS=2.302;HaplotypeScore=2.8318;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=0;MQRankSum=-1.049;QD=11.47;ReadPosRankSum=2.072;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,22:57:99:682,0,1070
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4005 chr1 150297 . T C 2289.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=59.46;MQ0=0;QD=28.40;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2318,175,0
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4006 chr1 150375 . T G 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.134;DP=48;Dels=0.00;FS=14.013;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-0.610;QD=14.87;ReadPosRankSum=0.735;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,22:48:99:742,0,881
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|
4007 chr1 150494 . A G 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.680;DP=38;Dels=0.00;FS=1.849;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=0.182;QD=25.63;ReadPosRankSum=1.541;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,28:38:99:1002,0,268
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|
4008 chr1 150499 . C A 217.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.340;DP=37;Dels=0.00;FS=1.885;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=1;MQRankSum=-0.698;QD=5.89;ReadPosRankSum=-1.378;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,10:37:99:246,0,955
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|
4009 chr1 150581 . C T 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.334;DP=28;Dels=0.00;FS=7.346;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.220;QD=6.46;ReadPosRankSum=-0.318;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:209,0,766
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|
4010 chr1 150588 . A T 1273.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.05;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1302,96,0
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|
4011 chr1 150606 . C T 1237.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.81;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1266,93,0
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|
4012 chr1 150717 . T A,G 1153.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;QD=32.04;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,16,20:36:99:1346,748,699,599,0,539
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4013 chr1 150752 . G A 1457.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.89;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1486,114,0
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|
4014 chr1 150838 . A G 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.568;DP=52;Dels=0.00;FS=6.106;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.029;QD=10.65;ReadPosRankSum=1.741;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,18:52:99:582,0,1173
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|
4015 chr1 150929 . G A 2230.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.19;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2259,172,0
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|
4016 chr1 150953 . C A 979.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.538;DP=60;Dels=0.00;FS=31.975;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.044;QD=16.33;ReadPosRankSum=-0.680;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,31:60:99:1008,0,1004
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|
4017 chr1 150957 . T C 1038.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.859;DP=61;Dels=0.00;FS=31.108;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.888;QD=17.03;ReadPosRankSum=-0.744;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,32:61:99:1067,0,979
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|
4018 chr1 151031 . T A 2189.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=0;QD=33.38;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2218,166,0
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4019 chr1 151074 . A T 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.170;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=1.9853;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-0.650;QD=16.10;ReadPosRankSum=-0.550;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:817,0,821
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4020 chr1 151153 . T A 762.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.182;DP=58;Dels=0.00;FS=7.584;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=0.355;QD=13.15;ReadPosRankSum=-0.087;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:791,0,1148
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|
4021 chr1 151277 . G C 328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.054;DP=35;Dels=0.00;FS=8.547;HaplotypeScore=3.9810;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.126;QD=9.39;ReadPosRankSum=0.811;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P284|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_151216_151324) GT:AD:DP:GQ:PL 0/1:22,12:35:99:357,0,750
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4022 chr1 151351 . A G 1121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.257;DP=53;Dels=0.00;FS=5.783;HaplotypeScore=5.9768;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.771;QD=21.17;ReadPosRankSum=-0.046;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,33:53:99:1150,0,663
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4023 chr1 151361 . A G,T 1601.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;QD=32.03;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,26,24:50:99:1836,882,804,954,0,882
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|
4024 chr1 151391 . T A 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.522;DP=43;Dels=0.00;FS=1.286;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.140;QD=10.46;ReadPosRankSum=-0.675;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,15:43:99:478,0,965
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|
4025 chr1 151489 . T C 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=53;Dels=0.00;FS=1.065;HaplotypeScore=1.9990;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.773;QD=17.41;ReadPosRankSum=-0.401;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:951,0,823
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|
4026 chr1 151542 . C T 1073.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.309;DP=63;Dels=0.00;FS=30.147;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.313;QD=17.04;ReadPosRankSum=-0.351;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,32:63:99:1102,0,1065
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|
4027 chr1 151610 . C A 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.325;DP=59;Dels=0.00;FS=9.684;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.218;QD=14.40;ReadPosRankSum=1.356;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,27:59:99:878,0,1066
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|
|
4028 chr1 151618 . T C 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.238;DP=61;Dels=0.00;FS=5.239;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.094;QD=16.44;ReadPosRankSum=0.815;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,31:61:99:1031,0,1031
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|
|
4029 chr1 151695 . T G 1036.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.206;DP=51;Dels=0.00;FS=1.161;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-1.688;QD=20.33;ReadPosRankSum=2.209;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1065,0,641
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|
|
4030 chr1 151785 . A G 2449.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.96;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2478,184,0
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|
|
4031 chr1 151923 . T C 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.913;DP=42;Dels=0.00;FS=6.816;HaplotypeScore=1.8662;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-0.225;QD=12.64;ReadPosRankSum=-0.225;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,17:42:99:559,0,782
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|
|
4032 chr1 151972 . A G 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.562;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=0.876;QD=17.48;ReadPosRankSum=-0.614;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:745,0,597
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|
|
4033 chr1 152191 . C G 1805.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9945;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=0;QD=30.22;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1834,147,0
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|
|
4034 chr1 152290 . A G 1160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.627;DP=72;Dels=0.00;FS=4.729;HaplotypeScore=2.7880;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-1.788;QD=16.12;ReadPosRankSum=1.604;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:36,35:72:99:1189,0,1208
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|
|
4035 chr1 152381 . C A 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.304;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-0.235;QD=10.50;ReadPosRankSum=-0.254;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,19:54:99:595,0,1229
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|
|
4036 chr1 152382 . C T 533.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.305;DP=53;Dels=0.00;FS=1.147;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.873;QD=10.07;ReadPosRankSum=-0.009;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:562,0,1258
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|
|
4037 chr1 152486 . A G 2355.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.88;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2384,181,0
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|
|
4038 chr1 152515 . T A 2726.77 . AC=2;AF=1.00;AN=2;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.81;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,69:69:99:2755,208,0
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|
|
4039 chr1 152581 . C A 2660.77 . AC=2;AF=1.00;AN=2;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.15;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,68:68:99:2689,202,0
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|
|
4040 chr1 152658 . A T 954.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.086;DP=65;Dels=0.00;FS=3.385;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.165;QD=14.69;ReadPosRankSum=-0.574;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:36,29:65:99:983,0,1258
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|
|
4041 chr1 152684 . C G 2666.77 . AC=2;AF=1.00;AN=2;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.01;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,68:68:99:2695,202,0
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|
|
4042 chr1 152720 . A G 1186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.493;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.563;QD=18.84;ReadPosRankSum=0.826;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,36:63:99:1215,0,861
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|
|
4043 chr1 152741 . G T 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.082;DP=61;Dels=0.00;FS=3.616;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.42;MQ0=1;MQRankSum=0.365;QD=13.05;ReadPosRankSum=-1.096;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,26:61:99:824,0,1171
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|
|
4044 chr1 152749 . T C 1986.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.667;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=2;MLEAF=1.00;MQ=55.72;MQ0=1;MQRankSum=-0.360;QD=25.29;ReadPosRankSum=0.033;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,53:54:99:2015,153,0
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|
|
4045 chr1 152752 . G C 2005.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=2;MLEAF=1.00;MQ=55.46;MQ0=1;QD=30.47;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2034,153,0
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|
|
4046 chr1 152755 . T C 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.197;DP=55;Dels=0.00;FS=3.860;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=55.24;MQ0=1;MQRankSum=2.481;QD=17.30;ReadPosRankSum=1.370;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:980,0,789
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|
|
4047 chr1 152892 . T C 96.28 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.44;MQ0=4;QD=10.70;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,9:9:9:124,9,0
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|
4048 chr1 152911 . G A 137.03 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.54;MQ0=4;QD=12.46;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,11:11:12:165,12,0
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|
4049 chr1 152938 . C T 136.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.683;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.60;MQ0=4;MQRankSum=1.683;QD=10.46;ReadPosRankSum=1.001;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:6,7:13:12:164,12,0
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|
4050 chr1 153166 . G A 87.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.250;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=5.7547;MLEAC=1;MLEAF=0.500;MQ=18.57;MQ0=5;MQRankSum=1.137;QD=2.93;ReadPosRankSum=1.137;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,10:30:92:116,0,92
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|
4051 chr1 153200 . C T 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.078;DP=33;Dels=0.00;FS=3.979;HaplotypeScore=1.7046;MLEAC=1;MLEAF=0.500;MQ=15.76;MQ0=8;MQRankSum=0.670;QD=1.11;ReadPosRankSum=1.136;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,10:33:65:65,0,140
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|
4052 chr1 153324 . A G 148.31 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.081;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=2.9300;MLEAC=1;MLEAF=0.500;MQ=13.59;MQ0=11;MQRankSum=2.944;QD=4.24;ReadPosRankSum=2.348;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:9,25:35:21:200,21,0
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|
4053 chr1 153381 . G A 41.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.203;DP=68;Dels=0.00;FS=15.911;HaplotypeScore=21.0001;MLEAC=1;MLEAF=0.500;MQ=12.66;MQ0=25;MQRankSum=0.041;QD=0.61;ReadPosRankSum=0.528;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:55,13:68:70:70,0,248
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|
4054 chr1 153430 . T C 161.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.369;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=1.7356;MLEAC=2;MLEAF=1.00;MQ=10.12;MQ0=25;MQRankSum=0.822;QD=3.68;ReadPosRankSum=-1.734;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:10,34:44:24:190,24,0
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|
4055 chr1 153445 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.027;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=9.0452;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=40;MQRankSum=-0.451;QD=0.83;ReadPosRankSum=0.239;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:55,12:67:84:84,0,310
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|
4056 chr1 153446 . C T 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.512;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=9.0452;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=40;MQRankSum=1.877;QD=0.65;ReadPosRankSum=-1.604;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:59,8:67:72:72,0,323
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|
4057 chr1 153476 . C T 447.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.346;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=14.6632;MLEAC=1;MLEAF=0.500;MQ=16.01;MQ0=39;MQRankSum=1.279;QD=5.89;ReadPosRankSum=0.316;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:41,35:76:79:476,0,79
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|
4058 chr1 153481 . G A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.783;DP=79;Dels=0.00;FS=2.335;HaplotypeScore=14.5114;MLEAC=1;MLEAF=0.500;MQ=15.99;MQ0=39;MQRankSum=0.178;QD=0.62;ReadPosRankSum=-0.285;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:67,12:79:77:77,0,497
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|
4059 chr1 153516 . G T 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.961;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=11.4714;MLEAC=1;MLEAF=0.500;MQ=16.93;MQ0=40;MQRankSum=1.294;QD=0.37;ReadPosRankSum=0.222;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:75,8:86:60:60,0,573
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|
4060 chr1 153518 . G A 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.813;DP=84;Dels=0.00;FS=0.000;HaplotypeScore=11.4714;MLEAC=1;MLEAF=0.500;MQ=17.03;MQ0=39;MQRankSum=1.715;QD=0.41;ReadPosRankSum=-1.174;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:72,12:84:63:63,0,569
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|
4061 chr1 153554 . T C 71.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.458;DP=51;Dels=0.00;FS=5.129;HaplotypeScore=5.7732;MLEAC=1;MLEAF=0.500;MQ=14.69;MQ0=20;MQRankSum=0.275;QD=1.41;ReadPosRankSum=-1.078;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,19:51:99:100,0,209
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|
4062 chr1 153590 . T C 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.398;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=7.8158;MLEAC=1;MLEAF=0.500;MQ=13.34;MQ0=22;MQRankSum=0.750;QD=1.69;ReadPosRankSum=0.824;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,41:74:99:153,0,172
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|
4063 chr1 153593 . T A 267.79 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.432;DP=73;Dels=0.00;FS=12.430;HaplotypeScore=16.3870;MLEAC=1;MLEAF=0.500;MQ=13.50;MQ0=20;MQRankSum=-2.002;QD=3.67;ReadPosRankSum=0.471;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:4,65:73:23:296,0,23
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|
4064 chr1 153603 . C T 519.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.475;DP=131;Dels=0.00;FS=1.943;HaplotypeScore=7.3720;MLEAC=1;MLEAF=0.500;MQ=19.19;MQ0=28;MQRankSum=1.316;QD=3.97;ReadPosRankSum=-2.546;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:83,47:131:99:548,0,748
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|
4065 chr1 153634 . C T 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.160;DP=250;Dels=0.00;FS=8.821;HaplotypeScore=55.7961;MLEAC=1;MLEAF=0.500;MQ=21.90;MQ0=51;MQRankSum=-0.113;QD=0.76;ReadPosRankSum=2.098;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:217,33:250:99:218,0,3652
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|
4066 chr1 153635 . A T 2861.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.523;DP=250;Dels=0.00;FS=76.787;HaplotypeScore=57.8078;MLEAC=1;MLEAF=0.500;MQ=22.51;MQ0=49;MQRankSum=3.056;QD=11.45;ReadPosRankSum=2.693;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:101,149:250:99:2890,0,1044
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|
|
4067 chr1 153682 . C T 171.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.146;DP=249;Dels=0.00;FS=4.305;HaplotypeScore=56.1815;MLEAC=1;MLEAF=0.500;MQ=24.41;MQ0=45;MQRankSum=2.445;QD=0.69;ReadPosRankSum=1.423;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:227,20:249:99:200,0,3583
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|
4068 chr1 153721 . C A 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.195;DP=246;Dels=0.00;FS=1.847;HaplotypeScore=63.1880;MLEAC=1;MLEAF=0.500;MQ=23.87;MQ0=46;MQRankSum=3.002;QD=0.06;ReadPosRankSum=-2.172;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:227,14:246:42:42,0,3329
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|
|
4069 chr1 153722 . G A 210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.376;DP=245;Dels=0.00;FS=1.279;HaplotypeScore=60.2739;MLEAC=1;MLEAF=0.500;MQ=23.89;MQ0=46;MQRankSum=2.339;QD=0.86;ReadPosRankSum=1.176;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:218,26:245:99:239,0,3144
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|
|
4070 chr1 153752 . T C 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.489;DP=115;Dels=0.00;FS=5.126;HaplotypeScore=12.2854;MLEAC=1;MLEAF=0.500;MQ=17.73;MQ0=25;MQRankSum=-2.081;QD=0.17;ReadPosRankSum=-1.203;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:75,40:115:48:48,0,900
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|
4071 chr1 153768 . A G 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.509;DP=106;Dels=0.00;FS=2.104;HaplotypeScore=3.8507;MLEAC=1;MLEAF=0.500;MQ=16.93;MQ0=30;MQRankSum=-0.643;QD=1.08;ReadPosRankSum=0.595;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:72,30:106:99:143,0,668
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|
|
4072 chr1 153796 . G A 1945.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.977;DP=209;Dels=0.00;FS=0.000;HaplotypeScore=23.0694;MLEAC=1;MLEAF=0.500;MQ=19.06;MQ0=44;MQRankSum=4.401;QD=9.31;ReadPosRankSum=0.585;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:85,120:209:99:1974,0,350
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|
|
4073 chr1 153918 . G A 20.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.717;DP=231;Dels=0.00;FS=102.092;HaplotypeScore=38.2429;MLEAC=1;MLEAF=0.500;MQ=21.52;MQ0=56;MQRankSum=1.367;QD=0.09;ReadPosRankSum=2.636;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:212,19:231:49:49,0,2890
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|
|
4074 chr1 153928 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=177;Dels=0.00;FS=70.822;HaplotypeScore=49.5301;MLEAC=1;MLEAF=0.500;MQ=19.80;MQ0=52;MQRankSum=2.469;QD=0.32;ReadPosRankSum=1.151;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:165,11:177:84:84,0,1870
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|
|
4075 chr1 153931 . G C 1198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.672;DP=171;Dels=0.00;FS=63.103;HaplotypeScore=41.3083;MLEAC=1;MLEAF=0.500;MQ=19.93;MQ0=50;MQRankSum=3.349;QD=7.01;ReadPosRankSum=-0.504;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:103,67:171:99:1227,0,745
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|
|
4076 chr1 153947 . A G 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.164;DP=117;Dels=0.00;FS=16.425;HaplotypeScore=22.7832;MLEAC=1;MLEAF=0.500;MQ=19.47;MQ0=38;MQRankSum=2.093;QD=2.57;ReadPosRankSum=-1.715;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:97,20:117:99:329,0,946
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|
|
4077 chr1 153962 . T C 390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.029;DP=76;Dels=0.00;FS=28.843;HaplotypeScore=13.6296;MLEAC=1;MLEAF=0.500;MQ=17.52;MQ0=25;MQRankSum=3.039;QD=5.14;ReadPosRankSum=-2.479;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:54,22:76:99:419,0,279
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|
|
4078 chr1 153982 . C G 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.240;DP=27;Dels=0.00;FS=10.000;HaplotypeScore=2.6670;MLEAC=1;MLEAF=0.500;MQ=11.06;MQ0=11;MQRankSum=2.285;QD=1.36;ReadPosRankSum=2.415;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,5:27:29:65,0,29
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|
|
4079 chr1 154000 . A C 52.28 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.44;MQ0=1;QD=8.71;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,6:6:9:80,9,0
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|
|
4080 chr1 154002 . G A 52.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.74;MQ0=1;QD=10.46;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:80,9,0
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|
|
4081 chr1 154038 . G A 30.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.736;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=18.18;MQ0=1;MQRankSum=0.736;QD=7.69;ReadPosRankSum=-0.736;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,3:4:6:58,6,0
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|
|
4082 chr1 154066 . G A 262.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.80;MQ0=2;QD=23.89;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,10:11:27:291,27,0
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|
|
4083 chr1 154073 . A T 236.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.80;MQ0=2;QD=21.53;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,10:11:24:265,24,0
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|
|
4084 chr1 154089 . C T 246.1 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.061;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.9468;MLEAC=1;MLEAF=0.500;MQ=27.14;MQ0=4;MQRankSum=2.003;QD=16.41;ReadPosRankSum=2.003;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:5,10:15:11:274,0,11
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|
4085 chr1 154114 . T C 272.41 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.778;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=25.10;MQ0=4;MQRankSum=2.024;QD=15.13;ReadPosRankSum=0.934;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:5,13:18:8:300,8,0
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|
|
4086 chr1 154133 . C T 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.115;DP=35;Dels=0.00;FS=9.558;HaplotypeScore=3.5584;MLEAC=1;MLEAF=0.500;MQ=18.65;MQ0=14;MQRankSum=2.353;QD=3.25;ReadPosRankSum=1.445;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,7:35:99:142,0,207
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|
|
4087 chr1 154140 . G A 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.437;DP=45;Dels=0.00;FS=11.635;HaplotypeScore=12.4237;MLEAC=1;MLEAF=0.500;MQ=18.93;MQ0=14;MQRankSum=2.372;QD=0.88;ReadPosRankSum=0.501;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,3:45:68:68,0,368
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|
|
4088 chr1 154141 . C T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.501;DP=45;Dels=0.00;FS=11.635;HaplotypeScore=12.4237;MLEAC=1;MLEAF=0.500;MQ=18.93;MQ0=14;MQRankSum=2.238;QD=0.88;ReadPosRankSum=0.167;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,3:45:68:68,0,372
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|
|
4089 chr1 154150 . C T 161.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.188;DP=52;Dels=0.00;FS=11.840;HaplotypeScore=12.4214;MLEAC=1;MLEAF=0.500;MQ=19.66;MQ0=15;MQRankSum=1.795;QD=3.11;ReadPosRankSum=-1.146;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:41,11:52:99:190,0,332
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|
|
4090 chr1 154162 . G A 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.044;DP=55;Dels=0.00;FS=11.710;HaplotypeScore=10.1969;MLEAC=1;MLEAF=0.500;MQ=18.76;MQ0=15;MQRankSum=2.642;QD=4.32;ReadPosRankSum=-0.664;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:43,12:55:99:266,0,265
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|
|
4091 chr1 154178 . A T 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.453;DP=57;Dels=0.00;FS=12.518;HaplotypeScore=35.4325;MLEAC=1;MLEAF=0.500;MQ=19.06;MQ0=14;MQRankSum=0.047;QD=0.65;ReadPosRankSum=0.421;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:49,8:57:65:65,0,554
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|
4092 chr1 154185 . G A 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.265;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=32.5155;MLEAC=1;MLEAF=0.500;MQ=19.28;MQ0=13;MQRankSum=-1.073;QD=0.29;ReadPosRankSum=-0.593;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:47,8:55:44:44,0,542
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|
4093 chr1 154186 . C T 307.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.791;DP=56;Dels=0.00;FS=6.576;HaplotypeScore=25.1706;MLEAC=1;MLEAF=0.500;MQ=19.31;MQ0=13;MQRankSum=2.199;QD=5.50;ReadPosRankSum=1.671;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,16:56:99:336,0,269
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|
4094 chr1 154211 . G T 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.560;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=20.8680;MLEAC=1;MLEAF=0.500;MQ=19.61;MQ0=12;MQRankSum=-1.269;QD=0.41;ReadPosRankSum=1.843;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:44,10:58:52:52,0,633
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|
4095 chr1 154212 . G A 44.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.108;DP=58;Dels=0.00;FS=23.517;HaplotypeScore=19.0376;MLEAC=1;MLEAF=0.500;MQ=19.61;MQ0=12;MQRankSum=0.000;QD=0.77;ReadPosRankSum=-1.855;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:48,10:58:73:73,0,611
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|
4096 chr1 154215 . A G 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.101;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=11.7095;MLEAC=1;MLEAF=0.500;MQ=19.47;MQ0=12;MQRankSum=-0.934;QD=0.60;ReadPosRankSum=2.084;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:45,10:55:61:61,0,555
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|
4097 chr1 154233 . T A 119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.328;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=4.6866;MLEAC=1;MLEAF=0.500;MQ=22.49;MQ0=0;MQRankSum=-1.708;QD=3.52;ReadPosRankSum=-1.604;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,16:34:99:148,0,338
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|
4098 chr1 154250 . A G 353.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=2.8562;MLEAC=2;MLEAF=1.00;MQ=21.26;MQ0=0;QD=20.81;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,17:17:45:382,45,0
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|
4099 chr1 154253 . T G 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.637;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=19.93;MQ0=0;MQRankSum=0.174;QD=6.85;ReadPosRankSum=0.637;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,7:15:99:131,0,128
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4100 chr1 154292 . T C 33.74 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.69;MQ0=3;QD=4.82;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:2,5:7:6:61,6,0
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4101 chr1 154334 . G A 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.692;DP=29;Dels=0.00;FS=9.558;HaplotypeScore=2.4530;MLEAC=1;MLEAF=0.500;MQ=23.50;MQ0=4;MQRankSum=-0.028;QD=4.34;ReadPosRankSum=-1.470;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:154,0,227
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|
4102 chr1 154358 . C A 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.756;DP=47;Dels=0.00;FS=6.284;HaplotypeScore=26.6661;MLEAC=1;MLEAF=0.500;MQ=23.42;MQ0=3;MQRankSum=-1.018;QD=0.26;ReadPosRankSum=-0.844;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:38,9:47:40:40,0,642
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|
4103 chr1 154359 . T G 544.14 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.915;DP=45;Dels=0.00;FS=12.648;HaplotypeScore=26.6661;MLEAC=1;MLEAF=0.500;MQ=23.92;MQ0=3;MQRankSum=0.678;QD=12.09;ReadPosRankSum=0.265;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:4,34:45:24:632,24,0
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|
4104 chr1 154370 . C A 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.646;DP=51;Dels=0.00;FS=8.661;HaplotypeScore=31.0665;MLEAC=1;MLEAF=0.500;MQ=23.78;MQ0=4;MQRankSum=-2.073;QD=0.43;ReadPosRankSum=1.470;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:38,13:51:50:50,0,714
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4105 chr1 154426 . G A 41.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.296;DP=49;Dels=0.00;FS=2.566;HaplotypeScore=5.9227;MLEAC=1;MLEAF=0.500;MQ=20.19;MQ0=9;MQRankSum=-0.765;QD=0.85;ReadPosRankSum=-0.359;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,10:49:70:70,0,505
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|
4106 chr1 154501 . C T 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.046;DP=30;Dels=0.00;FS=2.793;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=20.43;MQ0=7;MQRankSum=2.328;QD=1.86;ReadPosRankSum=-0.411;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,3:30:84:84,0,237
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4107 chr1 154559 . G A 70.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.761;DP=30;Dels=0.00;FS=8.741;HaplotypeScore=6.7678;MLEAC=1;MLEAF=0.500;MQ=21.74;MQ0=1;MQRankSum=1.761;QD=2.36;ReadPosRankSum=0.953;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,5:30:99:99,0,279
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4108 chr1 154589 . G A 67.03 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=15.06;MQ0=1;QD=7.45;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,9:9:12:95,12,0
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4109 chr1 154697 . A G 47.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=20.50;MQ0=0;QD=15.76;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:75,9,0
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|
4110 chr1 154715 . A G 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.988;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=24.23;MQ0=0;MQRankSum=0.406;QD=2.27;ReadPosRankSum=-0.406;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:3,3:7:44:44,0,65
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4111 chr1 154731 . T A 37.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.895;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=3.8976;MLEAC=1;MLEAF=0.500;MQ=22.58;MQ0=0;MQRankSum=1.214;QD=3.78;ReadPosRankSum=-1.214;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,3:10:66:66,0,111
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4112 chr1 154741 . G A 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.309;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=3.8993;MLEAC=1;MLEAF=0.500;MQ=21.34;MQ0=0;MQRankSum=-1.309;QD=1.82;ReadPosRankSum=0.135;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,5:12:50:50,0,124
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4113 chr1 154746 . C T 193.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=11.7238;MLEAC=2;MLEAF=1.00;MQ=21.34;MQ0=0;QD=16.15;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,12:12:24:222,24,0
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4114 chr1 154748 . G C 40.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.185;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=11.7238;MLEAC=1;MLEAF=0.500;MQ=21.34;MQ0=0;MQRankSum=1.664;QD=3.40;ReadPosRankSum=0.000;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,3:12:69:69,0,77
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|
4115 chr1 154754 . C T 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.246;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=7.8245;MLEAC=1;MLEAF=0.500;MQ=21.59;MQ0=0;MQRankSum=1.246;QD=2.34;ReadPosRankSum=0.000;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:11,3:14:61:61,0,161
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|
4116 chr1 154802 . G A 95.96 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.831;DP=13;Dels=0.00;FS=2.533;HaplotypeScore=2.9205;MLEAC=1;MLEAF=0.500;MQ=17.54;MQ0=1;MQRankSum=2.367;QD=7.38;ReadPosRankSum=0.135;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,7:13:5:123,0,5
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|
4117 chr1 154809 . G T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.768;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=2.9205;MLEAC=1;MLEAF=0.500;MQ=18.22;MQ0=1;MQRankSum=1.296;QD=1.24;ReadPosRankSum=-1.532;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,2:12:43:43,0,89
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|
4118 chr1 154987 . T C 21.77 LowQual AC=2;AF=1.00;AN=2;BaseQRankSum=0.751;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=1.6643;MLEAC=2;MLEAF=1.00;MQ=9.62;MQ0=4;MQRankSum=0.751;QD=1.67;ReadPosRankSum=0.751;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,12:13:6:49,6,0
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4119 chr1 155087 . G A 13.97 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=8.76;MQ0=18;MQRankSum=-0.736;QD=0.67;ReadPosRankSum=0.736;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:3,18:21:23:42,0,23
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4120 chr1 155148 . C T 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.005;DP=98;Dels=0.00;FS=2.718;HaplotypeScore=13.7215;MLEAC=1;MLEAF=0.500;MQ=23.52;MQ0=36;MQRankSum=0.569;QD=0.13;ReadPosRankSum=-1.756;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:89,8:98:41:41,0,1299
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4121 chr1 155229 . G A 480.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.42;MQ0=12;QD=10.93;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,44:44:51:509,51,0
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4122 chr1 155280 . G A 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.347;DP=131;Dels=0.00;FS=0.000;HaplotypeScore=11.9766;MLEAC=1;MLEAF=0.500;MQ=30.43;MQ0=12;MQRankSum=3.514;QD=1.38;ReadPosRankSum=-1.410;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:118,13:131:99:209,0,2278
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4123 chr1 155283 . G A 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.499;DP=138;Dels=0.00;FS=1.657;HaplotypeScore=13.9302;MLEAC=1;MLEAF=0.500;MQ=30.63;MQ0=13;MQRankSum=-1.295;QD=0.08;ReadPosRankSum=-0.289;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:125,13:138:39:39,0,2616
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4124 chr1 155314 . T C 2942.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.011;DP=180;Dels=0.00;FS=0.919;HaplotypeScore=9.2358;MLEAC=1;MLEAF=0.500;MQ=31.00;MQ0=20;MQRankSum=-4.581;QD=16.35;ReadPosRankSum=1.718;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,153:180:99:2971,0,552
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4125 chr1 155368 . C T 1195.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.080;DP=116;Dels=0.00;FS=10.244;HaplotypeScore=19.2230;MLEAC=1;MLEAF=0.500;MQ=26.70;MQ0=28;MQRankSum=-3.527;QD=10.31;ReadPosRankSum=-0.904;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,89:116:99:1224,0,527
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4126 chr1 155372 . G A 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.818;DP=110;Dels=0.00;FS=21.794;HaplotypeScore=22.7736;MLEAC=1;MLEAF=0.500;MQ=26.51;MQ0=28;MQRankSum=-2.154;QD=5.63;ReadPosRankSum=-1.004;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:54,56:110:99:648,0,967
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4127 chr1 155396 . T C 412.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.969;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=11.0107;MLEAC=1;MLEAF=0.500;MQ=20.74;MQ0=18;MQRankSum=0.787;QD=6.88;ReadPosRankSum=-2.546;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,42:60:99:441,0,159
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4128 chr1 155402 . T C 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.238;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=14.3324;MLEAC=1;MLEAF=0.500;MQ=18.93;MQ0=15;MQRankSum=0.120;QD=0.70;ReadPosRankSum=1.919;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:44,7:51:64:64,0,412
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4129 chr1 155404 . G A 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.763;DP=50;Dels=0.00;FS=2.315;HaplotypeScore=14.9975;MLEAC=1;MLEAF=0.500;MQ=18.26;MQ0=14;MQRankSum=-0.535;QD=2.86;ReadPosRankSum=0.049;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:171,0,293
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4130 chr1 155489 . G A 2696.77 . AC=2;AF=1.00;AN=2;DP=145;Dels=0.00;FS=0.000;HaplotypeScore=54.3672;MLEAC=2;MLEAF=1.00;MQ=28.17;MQ0=15;QD=18.60;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,143:145:99:2725,270,0
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4131 chr1 155496 . C T 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.978;DP=159;Dels=0.00;FS=16.800;HaplotypeScore=104.1353;MLEAC=1;MLEAF=0.500;MQ=28.15;MQ0=19;MQRankSum=4.281;QD=1.63;ReadPosRankSum=-1.263;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:142,17:159:99:287,0,2754
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4132 chr1 155542 . G A 286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=109;Dels=0.00;FS=13.436;HaplotypeScore=10.2277;MLEAC=1;MLEAF=0.500;MQ=25.34;MQ0=23;MQRankSum=3.323;QD=2.63;ReadPosRankSum=1.718;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:93,16:109:99:315,0,1464
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4133 chr1 155548 . C G 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.467;DP=104;Dels=0.00;FS=0.000;HaplotypeScore=19.0733;MLEAC=1;MLEAF=0.500;MQ=25.34;MQ0=22;MQRankSum=1.496;QD=0.18;ReadPosRankSum=0.594;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:92,9:104:47:47,0,1624
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4134 chr1 155558 . G A 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.354;DP=83;Dels=0.00;FS=2.807;HaplotypeScore=16.4098;MLEAC=1;MLEAF=0.500;MQ=23.92;MQ0=22;MQRankSum=-3.424;QD=6.50;ReadPosRankSum=-1.063;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,48:83:99:568,0,598
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4135 chr1 155561 . G A 244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.883;DP=74;Dels=0.00;FS=6.505;HaplotypeScore=10.4277;MLEAC=1;MLEAF=0.500;MQ=24.10;MQ0=19;MQRankSum=3.377;QD=3.31;ReadPosRankSum=0.558;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:63,11:74:99:273,0,780
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4136 chr1 155586 . T A 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.592;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=3.4598;MLEAC=1;MLEAF=0.500;MQ=17.41;MQ0=15;MQRankSum=1.659;QD=0.72;ReadPosRankSum=-0.829;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,3:33:52:52,0,180
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4137 chr1 155593 . G A 101.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.635;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=2;MLEAF=1.00;MQ=13.93;MQ0=11;MQRankSum=0.529;QD=4.39;ReadPosRankSum=-1.134;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:10,13:23:12:129,12,0
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4138 chr1 155655 . A G 941.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.704;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=3.7914;MLEAC=2;MLEAF=1.00;MQ=23.15;MQ0=4;MQRankSum=1.320;QD=18.11;ReadPosRankSum=-1.065;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:4,48:52:74:970,74,0
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4139 chr1 155704 . T C 886.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.9933;MLEAC=2;MLEAF=1.00;MQ=23.78;MQ0=5;QD=18.47;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,48:48:87:915,87,0
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4140 chr1 155711 . T C 319.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.006;DP=48;Dels=0.00;FS=10.017;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=23.78;MQ0=5;MQRankSum=-2.049;QD=6.66;ReadPosRankSum=2.024;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,27:48:99:348,0,395
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4141 chr1 155748 . G T 107.9 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.97;MQ0=2;QD=6.74;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,16:16:15:136,15,0
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4142 chr1 155814 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=12.84;MQ0=1;QD=6.21;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,6:6:9:65,9,0
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4143 chr1 155851 . A T 60.03 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=11.42;MQ0=4;QD=5.46;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,11:11:12:88,12,0
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4144 chr1 155852 . C T 60.03 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=10.93;MQ0=5;QD=5.00;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,11:12:12:88,12,0
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4145 chr1 155921 . C T 563.77 . AC=2;AF=1.00;AN=2;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=2.8662;MLEAC=2;MLEAF=1.00;MQ=13.15;MQ0=40;QD=6.96;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,81:81:69:592,69,0
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4146 chr1 156028 . T C 2144.77 . AC=2;AF=1.00;AN=2;DP=128;Dels=0.00;FS=0.000;HaplotypeScore=3.6927;MLEAC=2;MLEAF=1.00;MQ=20.13;MQ0=19;QD=16.76;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:3,124:128:99:2173,231,0
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4147 chr1 156056 . G A 1257.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.469;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=18.35;MQ0=26;MQRankSum=0.191;QD=12.97;ReadPosRankSum=0.052;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:12,85:97:99:1286,109,0
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4148 chr1 156246 . G A 1190.77 . AC=2;AF=1.00;AN=2;DP=78;Dels=0.00;FS=0.000;HaplotypeScore=2.8995;MLEAC=2;MLEAF=1.00;MQ=20.38;MQ0=6;QD=15.27;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,77:78:99:1219,129,0
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4149 chr1 156279 . C A 10.9 LowQual AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.91;MQ0=4;QD=1.09;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,10:10:3:37,3,0
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4150 chr1 156526 . A G 48.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.37;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0
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4151 chr1 156547 . A G 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.837;DP=56;Dels=0.00;FS=5.379;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=55.83;MQ0=1;MQRankSum=0.887;QD=14.50;ReadPosRankSum=1.631;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:840,0,999
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4152 chr1 156554 . T G 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.004;DP=67;Dels=0.00;FS=4.974;HaplotypeScore=1.7313;MLEAC=1;MLEAF=0.500;MQ=56.53;MQ0=1;MQRankSum=-1.187;QD=13.74;ReadPosRankSum=2.549;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,28:67:99:949,0,1225
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4153 chr1 156595 . T C 2518.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.62;MQ0=0;QD=29.54;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2547,190,0
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4154 chr1 156606 . A C 1350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.290;DP=67;Dels=0.00;FS=6.694;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.388;QD=20.16;ReadPosRankSum=2.689;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,39:67:99:1379,0,939
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4155 chr1 156782 . C T 914.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.833;DP=67;Dels=0.00;FS=3.401;HaplotypeScore=3.7879;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=1.087;QD=13.65;ReadPosRankSum=-1.036;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,28:67:99:943,0,1345
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4156 chr1 156846 . T A 1011.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=63;Dels=0.00;FS=3.924;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=2;MQRankSum=0.166;QD=16.06;ReadPosRankSum=2.460;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,32:63:99:1040,0,959
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4157 chr1 156855 . T C 1152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.634;DP=65;Dels=0.00;FS=9.722;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQ0=2;MQRankSum=-0.848;QD=17.73;ReadPosRankSum=1.937;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,35:65:99:1181,0,930
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4158 chr1 156873 . C A 440.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.088;DP=54;Dels=0.00;FS=4.462;HaplotypeScore=1.7781;MLEAC=1;MLEAF=0.500;MQ=57.51;MQ0=2;MQRankSum=-0.709;QD=8.16;ReadPosRankSum=0.210;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:54:99:469,0,1228
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4159 chr1 156909 . G C 813.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.429;DP=59;Dels=0.00;FS=5.572;HaplotypeScore=1.6553;MLEAC=1;MLEAF=0.500;MQ=56.17;MQ0=4;MQRankSum=0.042;QD=13.79;ReadPosRankSum=-0.951;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:842,0,823
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4160 chr1 156944 . G A 1215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=65;Dels=0.00;FS=0.962;HaplotypeScore=1.8316;MLEAC=1;MLEAF=0.500;MQ=58.32;MQ0=2;MQRankSum=-0.243;QD=18.70;ReadPosRankSum=1.160;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,37:65:99:1244,0,895
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4161 chr1 157008 . C T 1261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.015;DP=79;Dels=0.00;FS=7.743;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.24;MQ0=0;MQRankSum=1.211;QD=15.97;ReadPosRankSum=-0.240;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:40,39:79:99:1290,0,1323
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4162 chr1 157051 . C T 2830.77 . AC=2;AF=1.00;AN=2;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.18;MQ0=0;QD=28.67;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I320|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_157049_157117) GT:AD:DP:GQ:PL 1/1:0,74:74:99:2859,217,0
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4163 chr1 157058 . G A 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.588;DP=69;Dels=0.00;FS=2.053;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=0.597;QD=14.53;ReadPosRankSum=0.814;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E323K|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_157049_157117) GT:AD:DP:GQ:PL 0/1:38,31:69:99:1031,0,1223
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4164 chr1 157169 . C T 769.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.476;DP=58;Dels=0.00;FS=2.379;HaplotypeScore=1.9994;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=0.173;QD=13.27;ReadPosRankSum=0.973;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,25:58:99:798,0,1053
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4165 chr1 157239 . C T 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.399;DP=58;Dels=0.00;FS=11.764;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.039;QD=14.77;ReadPosRankSum=1.165;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:885,0,1106
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4166 chr1 157240 . T A 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.274;DP=58;Dels=0.00;FS=11.764;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.086;QD=14.63;ReadPosRankSum=1.196;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:877,0,1125
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|
|
4167 chr1 157275 . G A 1900.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.20;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1929,147,0
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|
4168 chr1 157331 . G A 1541.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.39;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1570,117,0
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|
|
4169 chr1 157449 . C G 1036.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.059;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=59.95;MQ0=0;MQRankSum=0.040;QD=18.19;ReadPosRankSum=-0.929;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1065,0,774
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|
|
4170 chr1 157515 . T A 1070.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.511;DP=64;Dels=0.00;FS=5.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.17;MQ0=0;MQRankSum=-0.839;QD=16.73;ReadPosRankSum=0.879;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,32:64:99:1099,0,1080
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|
|
4171 chr1 157636 . T G 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.766;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-0.591;QD=13.12;ReadPosRankSum=0.988;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,29:71:99:960,0,1393
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|
|
4172 chr1 157678 . C T 2841.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=1.8273;MLEAC=2;MLEAF=1.00;MQ=59.03;MQ0=0;QD=30.90;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,72:72:99:2870,214,0
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|
|
4173 chr1 157733 . T G 2546.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.75;MQ0=1;QD=32.27;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2575,190,0
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|
|
4174 chr1 157895 . A G 2244.77 . AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.96;MQ0=2;QD=30.24;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,58:58:99:2273,169,0
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|
|
4175 chr1 157961 . G A 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.614;DP=56;Dels=0.00;FS=2.293;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.124;QD=14.01;ReadPosRankSum=0.654;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:813,0,1117
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|
|
4176 chr1 158098 . C T 10.9 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.00;MQ0=0;QD=10.90;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,1:1:3:37,3,0
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|
|
4177 chr1 158261 . T A 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.358;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=23.67;MQ0=3;MQRankSum=1.231;QD=5.72;ReadPosRankSum=-1.231;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,2:8:28:74,0,28
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|
|
4178 chr1 158283 . C T 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.271;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=1.1567;MLEAC=1;MLEAF=0.500;MQ=14.13;MQ0=34;MQRankSum=1.733;QD=0.77;ReadPosRankSum=-1.733;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,2:44:62:62,0,105
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|
|
4179 chr1 158288 . C T 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.898;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=2.3135;MLEAC=1;MLEAF=0.500;MQ=14.13;MQ0=34;MQRankSum=1.733;QD=0.81;ReadPosRankSum=-0.898;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,2:44:64:64,0,104
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|
4180 chr1 158368 . A G 424.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.21;MQ0=0;QD=32.67;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,13:13:36:453,36,0
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|
4181 chr1 158427 . G A 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.660;DP=16;Dels=0.00;FS=17.404;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=31.30;MQ0=1;MQRankSum=0.505;QD=1.36;ReadPosRankSum=2.093;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,3:16:50:50,0,292
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|
4182 chr1 158461 . C A 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=16;Dels=0.00;FS=11.139;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=39.10;MQ0=1;MQRankSum=-1.083;QD=0.87;ReadPosRankSum=-0.505;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,4:16:42:42,0,369
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|
4183 chr1 158596 . T C 606.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.058;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.36;MQ0=5;MQRankSum=1.809;QD=18.96;ReadPosRankSum=0.444;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:4,28:32:32:635,32,0
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|
4184 chr1 158745 . A G 347.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.00;MQ0=3;QD=21.74;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,16:16:33:376,33,0
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4185 chr1 159147 . A G 38.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=19.37;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:66,6,0
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|
4186 chr1 159238 . C T 2056.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=60.21;MQ0=0;QD=32.71;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2085,157,0
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|
4187 chr1 159252 . G A 1542.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.28;MQ0=0;QD=33.84;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1571,117,0
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|
4188 chr1 159421 . C A 2132.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=26.0957;MLEAC=2;MLEAF=1.00;MQ=60.29;MQ0=0;QD=24.99;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2161,163,0
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|
4189 chr1 159489 . A C 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.295;DP=35;Dels=0.00;FS=5.503;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=-0.782;QD=9.99;ReadPosRankSum=0.122;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:378,0,778
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|
4190 chr1 159490 . G C 316.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.923;DP=36;Dels=0.00;FS=5.305;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.017;QD=8.80;ReadPosRankSum=0.285;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,12:36:99:345,0,811
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|
4191 chr1 159582 . A C 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.585;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.531;QD=16.89;ReadPosRankSum=0.155;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,34:64:99:1109,0,986
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4192 chr1 159628 . G A 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.490;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=1.246;QD=12.01;ReadPosRankSum=1.624;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:689,0,1123
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|
4193 chr1 159661 . T C 1693.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.35;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1722,132,0
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4194 chr1 159721 . T G 1542.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.26;MQ0=1;QD=30.48;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1571,120,0
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4195 chr1 159818 . G C 2039.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=58.07;MQ0=1;QD=29.67;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2068,157,0
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4196 chr1 159860 . A T 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.581;DP=31;Dels=0.00;FS=1.455;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.09;MQ0=1;MQRankSum=1.161;QD=15.99;ReadPosRankSum=-0.581;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,15:31:99:524,0,479
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4197 chr1 159991 . T A 2027.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=35.38;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:2056,154,0
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4198 chr1 160001 . G A 1962.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.39;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1991,147,0
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4199 chr1 160043 . A G 1679.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.51;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1708,126,0
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4200 chr1 160064 . A G 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=44;Dels=0.00;FS=4.575;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.662;QD=13.65;ReadPosRankSum=2.440;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:629,0,815
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4201 chr1 160171 . C A 1993.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.78;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gAt|A363D|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_160110_160217) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2022,156,0
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4202 chr1 160220 . A G 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.049;DP=63;Dels=0.00;FS=8.766;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=1;MQRankSum=0.585;QD=15.46;ReadPosRankSum=0.275;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:1002,0,1082
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4203 chr1 160223 . T C 2397.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.52;MQ0=1;QD=28.87;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,62:63:99:2426,184,0
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4204 chr1 160312 . T C 966.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.919;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=1;MQRankSum=0.460;QD=18.96;ReadPosRankSum=0.700;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,32:51:99:995,0,618
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4205 chr1 160344 . G T 996.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.378;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=1;MQRankSum=-0.844;QD=17.19;ReadPosRankSum=-1.600;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1025,0,815
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4206 chr1 160346 . C T 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.698;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=1;MQRankSum=-1.756;QD=18.01;ReadPosRankSum=-2.002;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1109,0,813
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4207 chr1 160403 . C T 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.418;DP=47;Dels=0.00;FS=2.597;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=1;MQRankSum=0.187;QD=15.87;ReadPosRankSum=1.792;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:774,0,801
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4208 chr1 160457 . T C 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.631;DP=50;Dels=0.00;FS=6.171;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=1;MQRankSum=-1.072;QD=15.06;ReadPosRankSum=-0.691;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:781,0,825
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4209 chr1 160628 . A G 1125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.790;DP=56;Dels=0.00;FS=3.920;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.486;QD=20.10;ReadPosRankSum=0.964;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1154,0,734
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4210 chr1 160653 . T C 936.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.121;DP=49;Dels=0.00;FS=2.547;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.131;QD=19.12;ReadPosRankSum=1.337;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:965,0,743
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4211 chr1 160771 . A G 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.517;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=0.483;QD=11.82;ReadPosRankSum=0.983;EFF=SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R393|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_160727_160819) GT:AD:DP:GQ:PL 0/1:20,15:35:99:442,0,684
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4212 chr1 160830 . T C 1740.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.72;MQ0=0;QD=32.09;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1769,129,0
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4213 chr1 160855 . T G 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.050;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.80;MQ0=0;MQRankSum=0.510;QD=16.59;ReadPosRankSum=0.790;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:841,0,789
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4214 chr1 160924 . A T 704.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.068;DP=45;Dels=0.00;FS=4.461;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=1;MQRankSum=0.305;QD=15.66;ReadPosRankSum=2.608;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:733,0,738
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4215 chr1 161085 . T C 995.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.826;DP=50;Dels=0.00;FS=4.041;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.708;QD=19.92;ReadPosRankSum=0.314;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:1024,0,658
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|
4216 chr1 161127 . C T 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.700;DP=43;Dels=0.00;FS=2.692;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.281;QD=14.51;ReadPosRankSum=0.159;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,19:43:99:652,0,837
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|
4217 chr1 161227 . G A 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.349;DP=54;Dels=0.00;FS=1.054;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.588;QD=17.01;ReadPosRankSum=1.522;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M421I|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161192_161296) GT:AD:DP:GQ:PL 0/1:27,27:54:99:947,0,859
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4218 chr1 161350 . A G 760.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.657;DP=58;Dels=0.00;FS=2.273;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=1;MQRankSum=-1.366;QD=13.12;ReadPosRankSum=0.024;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:789,0,1101
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4219 chr1 161518 . G T 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.065;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.343;QD=20.21;ReadPosRankSum=0.639;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1079,0,713
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4220 chr1 161550 . T G 2153.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2182,163,0
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4221 chr1 161583 . T C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.314;DP=48;Dels=0.00;FS=1.275;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.066;QD=17.70;ReadPosRankSum=-0.672;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:878,0,744
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|
4222 chr1 161598 . A G 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.153;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.505;QD=16.36;ReadPosRankSum=-0.176;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:748,0,762
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4223 chr1 161607 . G A 761.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.483;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=2.8660;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.527;QD=16.56;ReadPosRankSum=0.154;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:790,0,787
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4224 chr1 161743 . A C 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.492;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=1.6643;MLEAC=1;MLEAF=0.500;MQ=57.06;MQ0=1;MQRankSum=0.379;QD=15.60;ReadPosRankSum=-1.327;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K479Q|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:19,22:41:99:668,0,538
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4225 chr1 161769 . A T 896.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.793;DP=46;Dels=0.00;FS=9.187;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=1;MQRankSum=0.471;QD=19.49;ReadPosRankSum=0.172;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K487N|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:19,27:46:99:925,0,511
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4226 chr1 161794 . A C 607.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.236;DP=52;Dels=0.00;FS=10.280;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=56.58;MQ0=1;MQRankSum=-0.009;QD=11.69;ReadPosRankSum=-2.236;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Cta|I496L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:27,25:52:99:636,0,971
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4227 chr1 161795 . T A 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.758;DP=53;Dels=0.00;FS=10.399;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=56.65;MQ0=1;MQRankSum=-0.513;QD=12.26;ReadPosRankSum=-2.363;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aAa|I496K|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:27,26:53:99:678,0,963
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4228 chr1 161822 . C T 899.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.364;DP=66;Dels=0.00;FS=11.007;HaplotypeScore=3.5506;MLEAC=1;MLEAF=0.500;MQ=58.70;MQ0=1;MQRankSum=-1.119;QD=13.63;ReadPosRankSum=1.484;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P505L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:35,30:66:99:928,0,1200
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4229 chr1 161928 . A G 1788.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=59.37;MQ0=0;QD=29.28;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1817,138,0
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4230 chr1 162022 . A G 715.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.438;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=0.169;QD=11.01;ReadPosRankSum=1.409;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:40,25:65:99:744,0,1397
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|
4231 chr1 162207 . G A 2798.77 . AC=2;AF=1.00;AN=2;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.29;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,71:71:99:2827,214,0
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|
4232 chr1 162353 . G C 1411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.839;QD=20.46;ReadPosRankSum=0.322;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,42:69:99:1440,0,796
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4233 chr1 162433 . T G 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.759;DP=62;Dels=0.00;FS=3.875;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.175;QD=11.56;ReadPosRankSum=0.455;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:38,24:62:99:745,0,1353
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4234 chr1 162531 . C T 1811.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.50;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1840,141,0
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4235 chr1 162535 . G T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.412;DP=48;Dels=0.00;FS=1.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.094;QD=13.18;ReadPosRankSum=0.596;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,20:48:99:661,0,948
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4236 chr1 162542 . A C,T 1553.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;QD=32.36;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,28,20:48:99:1782,749,665,1033,0,973
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4237 chr1 162739 . G T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.537;DP=6;Dels=0.00;FS=10.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=0.406;QD=11.29;ReadPosRankSum=-1.537;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:3,3:6:45:96,0,45
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4238 chr1 162750 . G T 119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=8;Dels=0.00;FS=7.068;HaplotypeScore=2.9939;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=1.517;QD=14.97;ReadPosRankSum=-1.920;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:3,5:8:77:148,0,77
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4239 chr1 162805 . C T 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.349;DP=24;Dels=0.00;FS=6.214;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.920;QD=0.91;ReadPosRankSum=0.611;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,3:24:50:50,0,779
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4240 chr1 162820 . T C 161.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.584;DP=28;Dels=0.00;FS=7.181;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.539;QD=5.78;ReadPosRankSum=-2.122;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:190,0,773
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4241 chr1 162833 . A G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.944;DP=31;Dels=0.00;FS=12.129;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.218;QD=26.80;ReadPosRankSum=0.130;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,24:31:99:859,0,157
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4242 chr1 163107 . T C 1577.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.40;MQ0=1;QD=30.33;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1606,117,0
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4243 chr1 163152 . G C 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.018;DP=54;Dels=0.00;FS=5.807;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.98;MQ0=0;MQRankSum=0.996;QD=10.96;ReadPosRankSum=-0.127;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,19:54:99:620,0,1162
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4244 chr1 163218 . T G 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;DP=50;Dels=0.00;FS=3.842;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.806;QD=15.84;ReadPosRankSum=-0.456;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:820,0,917
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4245 chr1 163281 . T A 1020.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.585;DP=49;Dels=0.00;FS=5.959;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.365;QD=20.83;ReadPosRankSum=-0.133;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,30:49:99:1049,0,617
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4246 chr1 163602 . A T 1204.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.050;DP=60;Dels=0.00;FS=1.004;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.135;QD=20.08;ReadPosRankSum=-1.080;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1233,0,823
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4247 chr1 163615 . A C 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.427;DP=61;Dels=0.00;FS=0.975;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.905;QD=15.06;ReadPosRankSum=0.485;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,28:61:99:947,0,1113
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4248 chr1 163628 . T C 1045.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.228;DP=65;Dels=0.00;FS=0.942;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=-0.992;QD=16.09;ReadPosRankSum=0.046;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:34,31:65:99:1074,0,1122
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4249 chr1 163725 . C T 998.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.748;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=1;MQRankSum=1.996;QD=17.52;ReadPosRankSum=-0.090;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,30:57:99:1027,0,891
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4250 chr1 163736 . G C 1028.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=1;MQRankSum=-0.360;QD=17.74;ReadPosRankSum=-0.280;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1057,0,874
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4251 chr1 163748 . T G 2436.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.15;MQ0=1;QD=33.58;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:1,62:63:99:2465,187,0
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4252 chr1 163777 . C A 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.340;DP=58;Dels=0.00;FS=2.434;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=2;MQRankSum=0.445;QD=18.15;ReadPosRankSum=0.330;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1081,0,777
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4253 chr1 163806 . C T 826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=52;Dels=0.00;FS=4.176;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=1;MQRankSum=0.386;QD=15.90;ReadPosRankSum=0.763;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:855,0,885
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4254 chr1 163808 . A G 837.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.176;DP=49;Dels=0.00;FS=2.654;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=1;MQRankSum=-2.064;QD=17.10;ReadPosRankSum=0.186;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:866,0,770
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4255 chr1 163854 . A G 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.499;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=1;MQRankSum=-1.274;QD=13.14;ReadPosRankSum=0.742;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:646,0,892
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|
|
4256 chr1 163894 . A C 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.057;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.626;QD=14.66;ReadPosRankSum=0.011;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:688,0,813
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|
|
4257 chr1 163957 . T A 957.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.166;DP=61;Dels=0.00;FS=3.596;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.570;QD=15.70;ReadPosRankSum=-1.105;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,29:61:99:986,0,1103
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|
|
4258 chr1 163980 . A G 1028.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.148;DP=63;Dels=0.00;FS=3.778;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.763;QD=16.33;ReadPosRankSum=-1.010;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:1057,0,1126
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|
|
4259 chr1 164145 . A T 2835.77 . AC=2;AF=1.00;AN=2;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.01;MQ0=0;QD=32.13;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,74:74:99:2864,220,0
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|
|
4260 chr1 164203 . T G 1012.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.489;DP=77;Dels=0.00;FS=0.917;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.110;QD=13.15;ReadPosRankSum=1.352;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:44,33:77:99:1041,0,1470
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|
|
4261 chr1 164252 . A C 1239.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.049;DP=65;Dels=0.00;FS=3.361;HaplotypeScore=3.6644;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.297;QD=19.07;ReadPosRankSum=-0.284;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:29,36:65:99:1268,0,967
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|
|
4262 chr1 164282 . T G 1111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.437;DP=64;Dels=0.00;FS=8.767;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=59.69;MQ0=0;MQRankSum=-0.443;QD=17.37;ReadPosRankSum=0.484;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,33:64:99:1140,0,1007
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|
|
4263 chr1 164379 . G A 1256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.789;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=1.7845;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=1.487;QD=17.46;ReadPosRankSum=0.834;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,37:72:99:1285,0,1107
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|
|
4264 chr1 164466 . A T 2375.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.56;MQ0=0;QD=28.88;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2404,181,0
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|
|
4265 chr1 164494 . T C 612.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.288;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9829;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.082;QD=11.78;ReadPosRankSum=2.323;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,20:52:99:641,0,1102
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|
|
4266 chr1 164861 . T C 1256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.530;DP=68;Dels=0.00;FS=4.986;HaplotypeScore=1.9732;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-0.679;QD=18.48;ReadPosRankSum=-1.576;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,40:68:99:1285,0,918
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|
|
4267 chr1 164906 . A G 2110.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.84;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2139,163,0
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|
|
4268 chr1 164958 . A G 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.907;DP=50;Dels=0.00;FS=1.129;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=0.295;QD=12.86;ReadPosRankSum=-1.081;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:671,0,981
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|
|
4269 chr1 165095 . G A 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.403;DP=52;Dels=0.00;FS=2.379;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.531;QD=16.03;ReadPosRankSum=-0.751;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:862,0,944
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|
|
4270 chr1 165389 . T G 915.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.072;DP=62;Dels=0.00;FS=5.213;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.87;MQ0=0;MQRankSum=-2.850;QD=14.77;ReadPosRankSum=-1.735;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,29:62:99:944,0,1149
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|
|
4271 chr1 165407 . C A 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.847;DP=64;Dels=0.00;FS=2.112;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.97;MQ0=0;MQRankSum=-5.528;QD=13.62;ReadPosRankSum=-1.455;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:36,28:64:99:900,0,1192
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|
|
4272 chr1 165447 . A G 873.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.256;DP=49;Dels=0.00;FS=5.913;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.96;MQ0=0;MQRankSum=4.271;QD=17.83;ReadPosRankSum=-0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:902,0,692
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|
|
4273 chr1 165482 . G T 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.083;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=3.1091;MLEAC=1;MLEAF=0.500;MQ=54.61;MQ0=0;MQRankSum=-0.596;QD=13.47;ReadPosRankSum=0.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,19:42:99:594,0,720
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|
|
4274 chr1 165483 . G T 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.222;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=3.1091;MLEAC=1;MLEAF=0.500;MQ=54.70;MQ0=0;MQRankSum=-1.082;QD=15.12;ReadPosRankSum=0.196;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,21:41:99:648,0,635
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|
|
4275 chr1 165526 . C T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.827;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.764;QD=21.70;ReadPosRankSum=0.631;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:17,30:47:99:1048,0,485
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|
|
4276 chr1 165678 . C T 989.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.733;DP=56;Dels=0.00;FS=5.297;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=54.10;MQ0=0;MQRankSum=-3.048;QD=17.67;ReadPosRankSum=0.468;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,30:56:99:1018,0,833
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|
|
4277 chr1 165701 . T A 1032.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.604;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=55.17;MQ0=0;MQRankSum=-1.305;QD=19.86;ReadPosRankSum=0.839;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,31:52:99:1061,0,610
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|
|
4278 chr1 165957 . G A 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.556;DP=42;Dels=0.00;FS=6.343;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.657;QD=17.66;ReadPosRankSum=0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:770,0,629
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|
4279 chr1 165982 . T G 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.314;DP=35;Dels=0.00;FS=1.320;HaplotypeScore=2.6981;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-1.007;QD=15.28;ReadPosRankSum=-0.677;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:563,0,552
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|
4280 chr1 166129 . A T 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.425;DP=41;Dels=0.00;FS=4.533;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=-0.719;QD=14.24;ReadPosRankSum=2.261;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:612,0,716
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|
4281 chr1 166135 . T G 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=40;Dels=0.00;FS=4.837;HaplotypeScore=2.7214;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=0;MQRankSum=-1.300;QD=15.12;ReadPosRankSum=1.625;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:633,0,714
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|
|
4282 chr1 166157 . C T 309.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.204;DP=19;Dels=0.00;FS=17.041;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.70;MQ0=0;MQRankSum=1.592;QD=16.30;ReadPosRankSum=-0.122;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:9,10:19:99:338,0,285
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|
|
4283 chr1 166165 . G A 819.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=59.74;MQ0=0;QD=35.10;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:848,66,0
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|
4284 chr1 166187 . T C 745.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.71;MQ0=0;QD=23.25;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:774,60,0
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|
|
4285 chr1 166200 . C T 1299.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=13.5158;MLEAC=2;MLEAF=1.00;MQ=55.26;MQ0=0;QD=30.02;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1328,99,0
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|
4286 chr1 166214 . C T 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.550;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.69;MQ0=0;MQRankSum=-5.017;QD=10.28;ReadPosRankSum=-1.750;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,15:35:99:388,0,673
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4287 chr1 166219 . A G 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.058;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.67;MQ0=0;MQRankSum=-5.166;QD=12.70;ReadPosRankSum=-0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:498,0,722
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|
4288 chr1 166226 . G A 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.613;DP=35;Dels=0.00;FS=1.330;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-5.050;QD=14.16;ReadPosRankSum=1.043;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:524,0,649
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|
|
4289 chr1 166233 . G A 527.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.763;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=54.82;MQ0=0;MQRankSum=-4.961;QD=13.89;ReadPosRankSum=2.701;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:556,0,691
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|
|
4290 chr1 166248 . G A 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.442;DP=37;Dels=0.00;FS=2.870;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=56.38;MQ0=0;MQRankSum=-3.398;QD=13.51;ReadPosRankSum=2.423;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:528,0,645
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|
|
4291 chr1 166255 . A C 437.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.555;DP=34;Dels=0.00;FS=3.155;HaplotypeScore=13.4643;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=-3.919;QD=12.88;ReadPosRankSum=2.220;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,15:34:99:466,0,539
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|
|
4292 chr1 166256 . C T 475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.050;DP=35;Dels=0.00;FS=2.984;HaplotypeScore=14.4309;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=0;MQRankSum=-3.394;QD=13.59;ReadPosRankSum=2.003;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:504,0,583
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|
|
4293 chr1 166297 . G A 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.528;DP=52;Dels=0.00;FS=1.203;HaplotypeScore=4.3119;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=0;MQRankSum=-0.194;QD=19.76;ReadPosRankSum=0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1056,0,614
|
|
|
4294 chr1 166322 . T A 1149.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.604;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=1.305;QD=19.16;ReadPosRankSum=0.500;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,34:60:99:1178,0,786
|
|
|
4295 chr1 166453 . A G 939.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.040;DP=55;Dels=0.00;FS=9.665;HaplotypeScore=2.6999;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.583;QD=17.09;ReadPosRankSum=-2.426;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:968,0,816
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|
|
4296 chr1 166585 . G A 732.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.313;DP=56;Dels=0.00;FS=2.282;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.945;QD=13.09;ReadPosRankSum=0.923;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:761,0,1060
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|
|
4297 chr1 166654 . A T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.786;DP=46;Dels=0.00;FS=4.286;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=1;MQRankSum=-1.445;QD=16.45;ReadPosRankSum=0.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:785,0,700
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|
|
4298 chr1 166658 . T G 701.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.864;DP=44;Dels=0.00;FS=9.040;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=1;MQRankSum=-2.277;QD=15.95;ReadPosRankSum=0.572;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:730,0,641
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|
|
4299 chr1 166669 . G C 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.834;DP=42;Dels=0.00;FS=15.562;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=1;MQRankSum=-0.595;QD=17.68;ReadPosRankSum=-0.013;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:771,0,549
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|
|
4300 chr1 166716 . A G 732.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.762;DP=46;Dels=0.00;FS=4.124;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.93;MQ0=2;MQRankSum=-1.715;QD=15.93;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:761,0,715
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|
|
4301 chr1 166733 . T G 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.886;DP=52;Dels=0.00;FS=5.964;HaplotypeScore=1.7337;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=2;MQRankSum=-1.925;QD=13.15;ReadPosRankSum=0.362;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:712,0,936
|
|
|
4302 chr1 166734 . G T 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.213;DP=54;Dels=0.00;FS=5.816;HaplotypeScore=3.7324;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=2;MQRankSum=-2.232;QD=12.46;ReadPosRankSum=0.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,24:54:99:701,0,1010
|
|
|
4303 chr1 166737 . T C 665.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.734;DP=56;Dels=0.00;FS=5.681;HaplotypeScore=4.7320;MLEAC=1;MLEAF=0.500;MQ=56.63;MQ0=2;MQRankSum=-1.928;QD=11.89;ReadPosRankSum=1.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:694,0,1084
|
|
|
4304 chr1 166751 . A C 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.339;DP=57;Dels=0.00;FS=2.274;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=1;MQRankSum=-0.813;QD=14.42;ReadPosRankSum=0.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,27:57:99:850,0,1009
|
|
|
4305 chr1 166834 . G A 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=38;Dels=0.00;FS=25.349;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=1;MQRankSum=0.410;QD=15.34;ReadPosRankSum=0.167;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:611,0,646
|
|
|
4306 chr1 166877 . T A 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.197;DP=32;Dels=0.00;FS=21.686;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.083;QD=13.74;ReadPosRankSum=1.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:18,14:32:99:468,0,592
|
|
|
4307 chr1 166961 . T C 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.053;DP=32;Dels=0.00;FS=15.187;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.468;QD=8.99;ReadPosRankSum=1.769;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:316,0,780
|
|
|
4308 chr1 167041 . T A 743.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=16.8441;MLEAC=2;MLEAF=1.00;MQ=57.88;MQ0=0;QD=34.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:772,63,0
|
|
|
4309 chr1 167090 . C T 1469.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.69;MQ0=0;QD=28.97;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1498,114,0
|
|
|
4310 chr1 167165 . C T 1575.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=31.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1604,120,0
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|
|
4311 chr1 167170 . A C 1602.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.42;MQ0=0;QD=33.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1631,123,0
|
|
|
4312 chr1 167208 . G A 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.357;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.870;QD=12.28;ReadPosRankSum=1.405;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,19:46:99:593,0,944
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|
|
4313 chr1 167228 . C G 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=45;Dels=0.00;FS=2.529;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.633;QD=18.57;ReadPosRankSum=1.519;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:864,0,666
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|
|
4314 chr1 167283 . A G 824.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.416;DP=47;Dels=0.00;FS=13.823;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.906;QD=17.55;ReadPosRankSum=1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,25:47:99:853,0,735
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|
|
4315 chr1 167363 . T A 1954.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:1983,153,0
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|
|
4316 chr1 167371 . G A 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.085;DP=51;Dels=0.00;FS=2.387;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.897;QD=17.33;ReadPosRankSum=0.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:912,0,760
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|
|
4317 chr1 167399 . G T 890.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.694;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.632;QD=16.20;ReadPosRankSum=-0.531;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:919,0,873
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|
4318 chr1 167568 . C T 700.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.692;DP=47;Dels=0.00;FS=4.301;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.926;QD=14.91;ReadPosRankSum=-1.266;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:729,0,770
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|
|
4319 chr1 167574 . G T 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.354;DP=45;Dels=0.00;FS=4.485;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=0.580;QD=14.26;ReadPosRankSum=-1.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:670,0,813
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|
|
4320 chr1 167656 . G A 1543.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.41;MQ0=0;QD=29.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1572,123,0
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|
|
4321 chr1 167672 . C G 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.198;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=0;MQRankSum=-2.527;QD=11.41;ReadPosRankSum=-0.834;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:496,0,851
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|
|
4322 chr1 167681 . A T 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.107;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-0.635;QD=12.42;ReadPosRankSum=-1.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:649,0,985
|
|
|
4323 chr1 168087 . G A 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.081;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=2.7985;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=0.503;QD=14.59;ReadPosRankSum=0.781;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,21:47:99:714,0,900
|
|
|
4324 chr1 168095 . G C 862.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.150;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-1.112;QD=17.61;ReadPosRankSum=0.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:891,0,777
|
|
|
4325 chr1 168096 . G A 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.232;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.551;QD=14.46;ReadPosRankSum=-0.851;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:737,0,907
|
|
|
4326 chr1 168153 . A G 694.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=44;Dels=0.00;FS=6.747;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=1.608;QD=15.79;ReadPosRankSum=-0.065;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,22:44:99:723,0,628
|
|
|
4327 chr1 168196 . G A 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.243;DP=34;Dels=0.00;FS=3.353;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=0.659;QD=13.11;ReadPosRankSum=-0.069;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,15:34:99:474,0,581
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|
|
4328 chr1 168202 . G T 1401.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;QD=39.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1430,108,0
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|
|
4329 chr1 168341 . T C 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.086;DP=58;Dels=0.00;FS=1.012;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.993;QD=13.50;ReadPosRankSum=-0.649;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:811,0,1056
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|
|
4330 chr1 168360 . G T 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.648;DP=55;Dels=0.00;FS=2.266;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.955;QD=12.69;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,25:55:99:726,0,991
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|
|
4331 chr1 168533 . C T 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=0;MQRankSum=0.230;QD=11.62;ReadPosRankSum=-1.027;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P42L|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:21,16:37:99:458,0,718
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|
|
4332 chr1 168548 . A T 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.299;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=1.9991;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=0.239;QD=11.20;ReadPosRankSum=-0.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tTc|Y47F|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:23,15:38:99:454,0,793
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|
|
4333 chr1 168693 . T C 454.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.458;DP=42;Dels=0.00;FS=4.987;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=2;MQRankSum=-0.505;QD=10.83;ReadPosRankSum=2.382;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S95|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:26,15:42:99:483,0,823
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|
|
4334 chr1 168747 . A T 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.500;DP=48;Dels=0.00;FS=4.386;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQ0=1;MQRankSum=0.649;QD=14.06;ReadPosRankSum=-0.309;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggT|G113|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:25,23:48:99:703,0,783
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|
|
4335 chr1 168840 . T C 808.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.320;DP=52;Dels=0.00;FS=5.785;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=0;MQRankSum=1.858;QD=15.55;ReadPosRankSum=0.540;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:837,0,857
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|
|
4336 chr1 168897 . T C 843.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.871;DP=57;Dels=0.00;FS=5.456;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.07;MQ0=0;MQRankSum=0.583;QD=14.80;ReadPosRankSum=0.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,27:57:99:872,0,987
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|
|
4337 chr1 168928 . C T 2404.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=62.12;MQ0=0;QD=31.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,63:63:99:2433,184,0
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|
|
4338 chr1 168963 . A C 1092.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.126;DP=70;Dels=0.00;FS=0.909;HaplotypeScore=4.3674;MLEAC=1;MLEAF=0.500;MQ=61.66;MQ0=1;MQRankSum=1.602;QD=15.61;ReadPosRankSum=0.462;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,35:70:99:1121,0,1161
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|
|
4339 chr1 168974 . T C 245.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.577;DP=49;Dels=0.00;FS=5.429;HaplotypeScore=0.9332;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=1;MQRankSum=-4.252;QD=5.02;ReadPosRankSum=2.424;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:38,11:49:99:274,0,1377
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|
|
4340 chr1 168984 . G A 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.339;DP=50;Dels=0.00;FS=1.222;HaplotypeScore=2.6583;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=-3.464;QD=8.06;ReadPosRankSum=1.051;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:431,0,1261
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|
|
4341 chr1 169015 . C G 1930.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=1;QD=24.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:1959,147,0
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|
|
4342 chr1 169059 . T C 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.424;DP=48;Dels=0.00;FS=1.206;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.445;QD=9.25;ReadPosRankSum=2.069;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,15:48:99:472,0,1188
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|
|
4343 chr1 169061 . C T 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.010;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.503;QD=10.74;ReadPosRankSum=0.995;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,18:51:99:576,0,1182
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|
4344 chr1 169185 . G A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.050;DP=50;Dels=0.00;FS=4.235;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=0.980;QD=11.94;ReadPosRankSum=-1.594;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:625,0,1008
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|
4345 chr1 169348 . G T 2385.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2414,181,0
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|
|
4346 chr1 169423 . G A 589.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.535;DP=40;Dels=0.00;FS=4.763;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.324;QD=14.74;ReadPosRankSum=-0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:618,0,620
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|
|
4347 chr1 169424 . C T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.169;DP=40;Dels=0.00;FS=4.763;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.690;QD=14.42;ReadPosRankSum=0.014;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,21:40:99:605,0,616
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|
4348 chr1 169456 . C G 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.543;DP=47;Dels=0.00;FS=13.725;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=1;MQRankSum=-1.163;QD=13.68;ReadPosRankSum=0.388;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,21:47:99:671,0,799
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|
|
4349 chr1 169607 . G A 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.477;DP=58;Dels=0.00;FS=3.625;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.227;QD=14.24;ReadPosRankSum=1.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:854,0,1075
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|
|
4350 chr1 169642 . G A 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.356;DP=58;Dels=0.00;FS=3.717;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-0.639;QD=14.27;ReadPosRankSum=-0.998;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:856,0,1091
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|
|
4351 chr1 169648 . A G 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.575;DP=59;Dels=0.00;FS=5.223;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.312;QD=14.28;ReadPosRankSum=-0.616;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:871,0,1059
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|
|
4352 chr1 169705 . C T 813.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.854;DP=63;Dels=0.00;FS=0.971;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=58.48;MQ0=0;MQRankSum=-0.354;QD=12.92;ReadPosRankSum=0.979;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:36,27:63:99:842,0,1216
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|
4353 chr1 169719 . G A 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.216;DP=60;Dels=0.00;FS=0.971;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=1.529;QD=13.80;ReadPosRankSum=1.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:856,0,1191
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|
|
4354 chr1 169815 . T C 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.744;DP=85;Dels=0.00;FS=5.036;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=1;MQRankSum=-0.413;QD=6.71;ReadPosRankSum=-0.785;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:63,22:85:99:599,0,2148
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|
4355 chr1 169830 . T G 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.067;DP=82;Dels=0.00;FS=5.065;HaplotypeScore=4.3793;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=1;MQRankSum=0.781;QD=7.48;ReadPosRankSum=-0.522;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:58,24:82:99:642,0,1903
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|
4356 chr1 169867 . A T 1602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.283;DP=92;Dels=0.00;FS=3.988;HaplotypeScore=1.7331;MLEAC=1;MLEAF=0.500;MQ=57.78;MQ0=0;MQRankSum=0.596;QD=17.42;ReadPosRankSum=0.004;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:40,51:92:99:1631,0,1086
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|
|
4357 chr1 169896 . A G 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.532;DP=92;Dels=0.00;FS=1.896;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=-1.080;QD=8.30;ReadPosRankSum=0.557;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:65,27:92:99:792,0,2212
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|
|
4358 chr1 169909 . A G 1909.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.617;DP=89;Dels=0.00;FS=2.916;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=1.306;QD=21.46;ReadPosRankSum=-1.499;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,54:89:99:1938,0,1053
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|
|
4359 chr1 169968 . C T 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.404;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=24.7819;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.734;QD=6.51;ReadPosRankSum=1.116;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:72,23:95:99:647,0,2530
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|
|
4360 chr1 169972 . T C 2032.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.409;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=24.7819;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=-1.407;QD=20.53;ReadPosRankSum=0.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:37,62:99:99:2061,0,1189
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|
|
4361 chr1 169997 . G T 668.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.396;DP=92;Dels=0.00;FS=3.217;HaplotypeScore=46.8443;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=1.054;QD=7.27;ReadPosRankSum=-0.769;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:68,24:92:99:697,0,2342
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|
|
4362 chr1 170001 . A C 590.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.420;DP=93;Dels=0.00;FS=3.202;HaplotypeScore=65.8412;MLEAC=1;MLEAF=0.500;MQ=58.80;MQ0=0;MQRankSum=0.583;QD=6.35;ReadPosRankSum=-0.298;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:70,23:93:99:619,0,2321
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4363 chr1 170005 . T A 826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.574;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=62.8400;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=0.339;QD=9.09;ReadPosRankSum=1.319;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:60,31:91:99:855,0,2167
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|
4364 chr1 170011 . T A 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.010;DP=90;Dels=0.00;FS=3.403;HaplotypeScore=40.8458;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.801;QD=6.26;ReadPosRankSum=0.496;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:69,21:90:99:592,0,2430
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|
4365 chr1 170043 . G T 514.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.393;DP=92;Dels=0.00;FS=6.914;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-0.005;QD=5.60;ReadPosRankSum=0.648;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:72,20:92:99:543,0,2449
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4366 chr1 170079 . C T 325.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.269;DP=84;Dels=0.00;FS=36.316;HaplotypeScore=155.6412;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.479;QD=3.88;ReadPosRankSum=-1.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:69,15:84:99:354,0,2529
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|
|
4367 chr1 170134 . C T 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.806;DP=84;Dels=0.00;FS=25.920;HaplotypeScore=2.3987;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.915;QD=2.15;ReadPosRankSum=1.360;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:71,13:84:99:209,0,2556
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|
4368 chr1 170169 . T A 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.068;DP=75;Dels=0.00;FS=22.598;HaplotypeScore=2.7329;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.239;QD=2.08;ReadPosRankSum=1.348;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:65,10:75:99:184,0,2327
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4369 chr1 170210 . A C 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.379;DP=80;Dels=0.00;FS=12.034;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=1;MQRankSum=-0.591;QD=11.07;ReadPosRankSum=-0.955;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:50,30:80:99:914,0,1744
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4370 chr1 170224 . G A 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.075;DP=77;Dels=0.00;FS=12.005;HaplotypeScore=3.7332;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=1;MQRankSum=-0.353;QD=11.24;ReadPosRankSum=-0.225;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:48,29:77:99:894,0,1620
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|
4371 chr1 170239 . C A 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.912;DP=71;Dels=0.00;FS=8.610;HaplotypeScore=2.7334;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=1;MQRankSum=-0.098;QD=11.11;ReadPosRankSum=1.434;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:45,26:71:99:817,0,1578
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|
4372 chr1 170266 . C T 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.026;DP=73;Dels=0.00;FS=0.000;HaplotypeScore=4.0879;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=-1.051;QD=9.33;ReadPosRankSum=0.076;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:49,24:73:99:709,0,1696
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|
4373 chr1 170289 . A G 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.276;DP=77;Dels=0.00;FS=2.006;HaplotypeScore=1.7803;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=-0.339;QD=9.96;ReadPosRankSum=-2.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:51,26:77:99:795,0,1734
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|
4374 chr1 170303 . G A 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=63;Dels=0.00;FS=33.610;HaplotypeScore=17.9844;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.166;QD=5.60;ReadPosRankSum=2.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,16:63:99:381,0,1693
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|
4375 chr1 170304 . A G 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.845;DP=63;Dels=0.00;FS=8.306;HaplotypeScore=17.9844;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.545;QD=6.76;ReadPosRankSum=0.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,16:63:99:454,0,1606
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|
4376 chr1 170360 . C T 818.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.394;DP=63;Dels=0.00;FS=0.955;HaplotypeScore=2.5184;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.256;QD=13.00;ReadPosRankSum=0.740;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,28:63:99:847,0,1189
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|
4377 chr1 170364 . C G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.042;DP=59;Dels=0.00;FS=2.175;HaplotypeScore=2.5184;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=0.510;QD=14.08;ReadPosRankSum=0.936;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:859,0,1076
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4378 chr1 170366 . C T 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=59;Dels=0.00;FS=1.010;HaplotypeScore=2.5184;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.234;QD=14.39;ReadPosRankSum=0.842;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,27:59:99:877,0,1076
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4379 chr1 170381 . C T 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.037;DP=59;Dels=0.00;FS=9.493;HaplotypeScore=9.7866;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.356;QD=11.00;ReadPosRankSum=-0.214;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:38,21:59:99:677,0,1290
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4380 chr1 170382 . G A 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.535;DP=59;Dels=0.00;FS=7.433;HaplotypeScore=10.7863;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.341;QD=3.44;ReadPosRankSum=0.302;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:48,11:59:99:231,0,1765
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4381 chr1 170393 . T A 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.295;DP=67;Dels=0.00;FS=1.050;HaplotypeScore=21.7756;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=0.059;QD=12.73;ReadPosRankSum=0.008;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:29,26:67:99:881,0,961
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4382 chr1 170403 . C A 345.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.760;DP=68;Dels=0.00;FS=2.482;HaplotypeScore=25.9777;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-0.799;QD=5.08;ReadPosRankSum=0.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:53,15:68:99:374,0,1880
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4383 chr1 170482 . T C 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;DP=57;Dels=0.00;FS=11.052;HaplotypeScore=19.8261;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=-0.166;QD=8.54;ReadPosRankSum=0.166;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:40,17:57:99:515,0,1440
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4384 chr1 170483 . C T 496.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.764;DP=54;Dels=0.00;FS=14.133;HaplotypeScore=21.8256;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-1.397;QD=9.20;ReadPosRankSum=-0.317;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:525,0,1294
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4385 chr1 170487 . A G 170.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.205;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=21.8256;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=0.892;QD=3.05;ReadPosRankSum=-0.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,9:56:99:199,0,1721
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4386 chr1 170502 . T C 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.810;DP=57;Dels=0.00;FS=1.273;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=0.354;QD=4.54;ReadPosRankSum=-1.122;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:46,11:57:99:287,0,1595
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4387 chr1 170515 . G C 394.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.903;DP=63;Dels=0.00;FS=10.967;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-2.124;QD=6.27;ReadPosRankSum=1.540;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,16:63:99:423,0,1617
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4388 chr1 170578 . C G 538.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.209;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=32.9738;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=1.493;QD=8.29;ReadPosRankSum=-0.627;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:46,19:65:99:567,0,1665
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4389 chr1 170582 . C T 466.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.246;DP=65;Dels=0.00;FS=12.918;HaplotypeScore=32.9738;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.097;QD=7.18;ReadPosRankSum=2.829;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:495,0,1695
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4390 chr1 170584 . C T 1141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=66;Dels=0.00;FS=3.389;HaplotypeScore=31.9744;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.899;QD=17.30;ReadPosRankSum=2.390;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1170,0,1057
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4391 chr1 170628 . C T 912.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.299;DP=67;Dels=0.00;FS=2.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=0.483;QD=13.62;ReadPosRankSum=0.659;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,32:67:99:941,0,1173
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4392 chr1 170648 . G A 118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.908;DP=67;Dels=0.00;FS=6.632;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.90;MQ0=0;MQRankSum=-1.055;QD=1.77;ReadPosRankSum=1.823;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:55,12:67:99:147,0,1992
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4393 chr1 170807 . C G 863.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.270;DP=63;Dels=0.00;FS=8.737;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=0.906;QD=13.71;ReadPosRankSum=-0.546;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:35,28:63:99:892,0,1101
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4394 chr1 170817 . G A 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.267;DP=59;Dels=0.00;FS=3.720;HaplotypeScore=21.9878;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=0.618;QD=13.42;ReadPosRankSum=0.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:33,26:59:99:820,0,1062
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4395 chr1 170849 . A T 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.123;DP=51;Dels=0.00;FS=13.682;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.123;QD=15.02;ReadPosRankSum=0.426;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:794,0,925
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4396 chr1 170873 . A T 1038.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.666;DP=58;Dels=0.00;FS=17.770;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=0.826;QD=17.91;ReadPosRankSum=-1.590;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1067,0,865
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4397 chr1 170879 . G A 987.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.614;DP=59;Dels=0.00;FS=14.005;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.493;QD=16.74;ReadPosRankSum=-0.538;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1016,0,929
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4398 chr1 170937 . C G 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.022;DP=60;Dels=0.00;FS=5.062;HaplotypeScore=3.7392;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=1.504;QD=15.53;ReadPosRankSum=-1.652;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:32,28:60:99:960,0,1076
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4399 chr1 170995 . G T 921.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.784;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=0;MQRankSum=-1.752;QD=18.44;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,27:50:99:950,0,694
|
|
|
4400 chr1 171012 . A G 1169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.147;DP=55;Dels=0.00;FS=2.354;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-2.330;QD=21.27;ReadPosRankSum=1.308;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:1198,0,645
|
|
|
4401 chr1 171029 . C T 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.183;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9467;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-3.183;QD=20.21;ReadPosRankSum=2.472;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,34:52:99:1079,0,514
|
|
|
4402 chr1 171034 . A G 1294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.637;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.9467;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-1.803;QD=23.54;ReadPosRankSum=1.874;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,37:55:99:1323,0,554
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|
|
4403 chr1 171062 . A G 1228.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.366;DP=52;Dels=0.00;FS=2.506;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-3.024;QD=23.63;ReadPosRankSum=-0.527;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,35:52:99:1257,0,545
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|
|
4404 chr1 171065 . C A 1210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.009;DP=51;Dels=0.00;FS=2.449;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=-1.908;QD=23.74;ReadPosRankSum=-0.689;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,34:51:99:1239,0,544
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|
|
4405 chr1 171068 . G T 1269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.744;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-1.725;QD=23.96;ReadPosRankSum=-1.153;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,36:53:99:1298,0,506
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|
|
4406 chr1 171215 . C T 1231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.054;DP=66;Dels=0.00;FS=2.128;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=0.155;QD=18.66;ReadPosRankSum=1.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:29,37:66:99:1260,0,877
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|
|
4407 chr1 171376 . A G 2221.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.05;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2250,169,0
|
|
|
4408 chr1 171546 . A T 929.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.055;DP=52;Dels=0.00;FS=1.174;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.350;QD=17.88;ReadPosRankSum=-1.345;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,29:52:99:958,0,752
|
|
|
4409 chr1 171611 . A G 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.465;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.578;QD=15.99;ReadPosRankSum=-0.148;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:748,0,784
|
|
|
4410 chr1 171683 . C T 1678.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1707,132,0
|
|
|
4411 chr1 171685 . A G 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.679;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.182;QD=15.73;ReadPosRankSum=1.811;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:689,0,730
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|
|
4412 chr1 171706 . C G 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.897;DP=45;Dels=0.00;FS=1.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.351;QD=15.73;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:736,0,753
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|
|
4413 chr1 171990 . G T 2282.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.11;MQ0=0;QD=29.50;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2311,172,0
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|
|
4414 chr1 172009 . G A 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.720;DP=61;Dels=0.00;FS=11.177;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=0.109;QD=12.93;ReadPosRankSum=-0.605;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:35,26:61:99:817,0,1209
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|
|
4415 chr1 172061 . A G 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.707;DP=51;Dels=0.00;FS=18.810;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=1.159;QD=15.94;ReadPosRankSum=1.837;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:841,0,812
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|
|
4416 chr1 172078 . G A 1642.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.98;MQ0=0;QD=30.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1671,129,0
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|
|
4417 chr1 172093 . C T 770.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.124;DP=35;Dels=0.00;FS=3.303;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=0.728;QD=22.02;ReadPosRankSum=0.444;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:11,24:35:99:799,0,305
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|
|
4418 chr1 172108 . C T 56.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.397;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=32.9713;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=-1.397;QD=2.10;ReadPosRankSum=-0.826;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,7:27:85:85,0,539
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|
4419 chr1 172146 . G C 1035.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=28.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aGg|T826R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1064,84,0
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|
4420 chr1 172150 . T C 1050.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=25.44;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I825V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,30:30:87:1079,87,0
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|
4421 chr1 172178 . T C 1336.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.42;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P815|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1365,114,0
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|
4422 chr1 172179 . G C 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.629;DP=38;Dels=0.00;FS=9.942;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.716;QD=12.55;ReadPosRankSum=1.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cGa|P815R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:20,18:38:99:505,0,656
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|
4423 chr1 172203 . G A 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.094;DP=46;Dels=0.00;FS=11.390;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=-2.028;QD=12.73;ReadPosRankSum=0.233;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S807L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,20:46:99:614,0,792
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|
4424 chr1 172283 . C T 303.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.164;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.63;MQ0=0;MQRankSum=-0.747;QD=9.21;ReadPosRankSum=-0.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G780|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:19,14:33:99:332,0,598
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|
|
4425 chr1 172319 . A G 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.142;DP=33;Dels=0.00;FS=1.475;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.46;MQ0=1;MQRankSum=0.833;QD=22.99;ReadPosRankSum=0.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S768|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:10,23:33:99:787,0,281
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|
|
4426 chr1 172364 . T C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.018;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=1;MQRankSum=0.201;QD=23.02;ReadPosRankSum=-0.128;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P753|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:10,26:36:99:857,0,295
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|
4427 chr1 172459 . T C 898.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.971;DP=43;Dels=0.00;FS=14.539;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=1;MQRankSum=0.000;QD=20.90;ReadPosRankSum=0.289;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I722V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:16,27:43:99:927,0,470
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|
4428 chr1 172499 . A G 1675.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.64;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L708|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1704,129,0
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|
|
4429 chr1 172613 . G C 2055.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=57.02;MQ0=0;QD=34.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L670|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2084,162,0
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|
|
4430 chr1 172721 . A G 739.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.419;DP=52;Dels=0.00;FS=10.166;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=0.276;QD=14.23;ReadPosRankSum=-0.958;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D634|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,23:52:99:768,0,1005
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|
4431 chr1 172810 . T C 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.584;DP=54;Dels=0.00;FS=5.733;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=1;MQRankSum=0.733;QD=10.96;ReadPosRankSum=0.362;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S605G|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:35,19:54:99:620,0,1125
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|
|
4432 chr1 173004 . G A 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.902;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-1.007;QD=16.90;ReadPosRankSum=0.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T540I|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:19,22:41:99:721,0,631
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|
|
4433 chr1 173180 . C T 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.102;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.132;QD=14.91;ReadPosRankSum=1.155;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S481|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:20,18:38:99:595,0,656
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|
|
4434 chr1 173273 . A C 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.237;DP=55;Dels=0.00;FS=3.786;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.026;QD=19.10;ReadPosRankSum=-0.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|cgT/cgG|R450|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1079,0,685
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|
|
4435 chr1 173338 . C G 770.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.117;DP=53;Dels=0.00;FS=1.043;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.759;QD=14.54;ReadPosRankSum=-1.349;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ctt|V429L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,24:53:99:799,0,968
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|
|
4436 chr1 173346 . C T 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.557;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.210;QD=13.37;ReadPosRankSum=-0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G426E|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:31,23:54:99:750,0,981
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|
|
4437 chr1 173348 . A G 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.312;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.467;QD=12.61;ReadPosRankSum=-0.220;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N425|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:32,22:54:99:709,0,1099
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4438 chr1 173405 . A G 535.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.617;DP=42;Dels=0.00;FS=9.292;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-1.162;QD=12.76;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L406|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,19:42:99:564,0,777
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|
4439 chr1 173410 . C T 823.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.566;DP=46;Dels=0.00;FS=8.606;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.794;QD=17.91;ReadPosRankSum=0.243;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V405I|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:21,25:46:99:852,0,607
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4440 chr1 173421 . C A 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.194;DP=45;Dels=0.00;FS=11.272;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=0.582;QD=13.37;ReadPosRankSum=-0.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tTg|W401L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:25,20:45:99:630,0,843
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4441 chr1 173444 . G A 516.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=48;Dels=0.00;FS=1.134;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-0.970;QD=10.77;ReadPosRankSum=0.696;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I393|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,19:48:99:545,0,1014
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4442 chr1 173446 . T C 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.885;DP=49;Dels=0.00;FS=2.535;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=-1.190;QD=11.95;ReadPosRankSum=0.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I393V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,20:49:99:614,0,949
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4443 chr1 173456 . G C 1836.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=58.90;MQ0=0;QD=29.53;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L389|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1865,141,0
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4444 chr1 173462 . A G 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.354;DP=52;Dels=0.00;FS=5.860;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.951;QD=11.80;ReadPosRankSum=0.186;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N387|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:31,21:52:99:642,0,1078
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4445 chr1 173510 . C T 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.000;DP=53;Dels=0.00;FS=1.110;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=2;MQRankSum=-0.086;QD=9.45;ReadPosRankSum=-0.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P371|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:30,23:53:99:529,0,994
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|
|
4446 chr1 173561 . T C 786.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.704;DP=55;Dels=0.00;FS=1.072;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=57.65;MQ0=2;MQRankSum=0.864;QD=14.30;ReadPosRankSum=0.027;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K354|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:28,27:55:99:815,0,864
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4447 chr1 173585 . G A 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=52;Dels=0.00;FS=2.386;HaplotypeScore=2.7882;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=1;MQRankSum=-1.379;QD=11.82;ReadPosRankSum=0.561;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I346|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:30,22:52:99:643,0,934
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|
4448 chr1 173596 . C A 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.149;DP=52;Dels=0.00;FS=1.065;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=1;MQRankSum=-0.331;QD=17.67;ReadPosRankSum=0.407;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A343S|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,29:52:99:947,0,721
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4449 chr1 173627 . A G 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.524;DP=52;Dels=0.00;FS=1.082;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=1;MQRankSum=0.180;QD=16.84;ReadPosRankSum=-0.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L332|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,29:52:99:904,0,775
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|
4450 chr1 173642 . A T 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.002;DP=46;Dels=0.00;FS=6.250;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.935;QD=13.82;ReadPosRankSum=0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A327|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:24,22:46:99:664,0,819
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|
4451 chr1 173687 . T C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.329;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.658;QD=14.97;ReadPosRankSum=0.094;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G312|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,21:44:99:687,0,788
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|
4452 chr1 173717 . A G 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.077;DP=36;Dels=0.00;FS=4.925;HaplotypeScore=1.7323;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.982;QD=17.52;ReadPosRankSum=0.982;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D302|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:17,19:36:99:659,0,518
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4453 chr1 173759 . C T 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.765;DP=43;Dels=0.00;FS=6.309;HaplotypeScore=1.8237;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.154;QD=15.46;ReadPosRankSum=-0.158;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E288|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:22,21:43:99:693,0,696
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4454 chr1 173818 . C A 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.603;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=-1.032;QD=15.94;ReadPosRankSum=-1.071;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A269S|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,27:50:99:825,0,741
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4455 chr1 173846 . G A 1783.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=28.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S259|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1812,141,0
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4456 chr1 173921 . G A 1387.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.71;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L234|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1416,105,0
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4457 chr1 173942 . C T 1229.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=37.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S227|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1258,93,0
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4458 chr1 173991 . T A 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.583;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-1.550;QD=13.08;ReadPosRankSum=0.583;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cTg|Q211L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:20,15:35:99:486,0,659
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4459 chr1 174026 . G T 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.138;DP=42;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.579;QD=14.71;ReadPosRankSum=1.484;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agA|S199R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:21,21:42:99:646,0,703
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4460 chr1 174172 . T A 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.056;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.22;MQ0=0;MQRankSum=-1.622;QD=1.68;ReadPosRankSum=-3.635;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Tgc|S151C|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:43,7:50:99:112,0,1507
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4461 chr1 174192 . G A 157.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.321;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=0;MQRankSum=-1.855;QD=3.51;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T144M|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:37,8:45:99:186,0,1296
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4462 chr1 174204 . T C 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.410;DP=46;Dels=0.00;FS=1.159;HaplotypeScore=5.9821;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=1.606;QD=12.86;ReadPosRankSum=-1.451;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H140R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,20:46:99:620,0,865
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4463 chr1 174214 . T G 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.366;DP=37;Dels=0.00;FS=1.982;HaplotypeScore=7.7151;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=-0.595;QD=1.37;ReadPosRankSum=2.653;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K137Q|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:31,5:37:79:79,0,1105
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4464 chr1 174232 . C T 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.406;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-1.789;QD=3.93;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G131S|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:27,7:34:99:162,0,947
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4465 chr1 174240 . G A 95.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.038;DP=32;Dels=0.00;FS=1.814;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-2.100;QD=2.99;ReadPosRankSum=0.941;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P128L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,6:32:99:124,0,917
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4466 chr1 174248 . G A 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.044;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=-3.194;QD=1.13;ReadPosRankSum=0.917;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G125|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:25,4:29:61:61,0,891
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4467 chr1 174251 . C T 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=-3.203;QD=0.99;ReadPosRankSum=0.885;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q124|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,4:30:58:58,0,916
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|
|
4468 chr1 174253 . G T 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.194;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-3.037;QD=1.88;ReadPosRankSum=0.853;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Aag|Q124K|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,4:27:79:79,0,826
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4469 chr1 174257 . G A 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.102;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.91;MQ0=0;MQRankSum=-3.037;QD=1.77;ReadPosRankSum=1.263;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H122|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,4:27:76:76,0,816
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|
|
4470 chr1 174272 . G A 78.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.316;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.55;MQ0=0;MQRankSum=-3.196;QD=2.54;ReadPosRankSum=1.370;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D117|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,5:31:99:107,0,934
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|
|
4471 chr1 174280 . G T 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.297;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.63;MQ0=0;MQRankSum=-3.218;QD=2.37;ReadPosRankSum=1.090;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Atg|L115M|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:27,5:32:99:104,0,957
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|
4472 chr1 174286 . G C 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.671;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=0;MQRankSum=-3.303;QD=2.44;ReadPosRankSum=0.510;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L113V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,5:31:99:104,0,936
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|
4473 chr1 174310 . C T 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.871;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=9.6555;MLEAC=1;MLEAF=0.500;MQ=55.07;MQ0=0;MQRankSum=-2.399;QD=19.31;ReadPosRankSum=-1.013;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A105T|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:11,24:35:99:704,0,322
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|
4474 chr1 174313 . G C 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.709;DP=37;Dels=0.00;FS=2.191;HaplotypeScore=9.6555;MLEAC=1;MLEAF=0.500;MQ=55.34;MQ0=0;MQRankSum=-2.812;QD=0.59;ReadPosRankSum=-0.024;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Gtc|L104V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:33,4:37:50:50,0,1107
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|
4475 chr1 174316 . C T 20.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.660;DP=37;Dels=0.00;FS=2.191;HaplotypeScore=9.9900;MLEAC=1;MLEAF=0.500;MQ=55.34;MQ0=0;MQRankSum=-2.812;QD=0.56;ReadPosRankSum=-0.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V103I|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:33,4:37:49:49,0,1123
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|
4476 chr1 174328 . C T 16.86 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.240;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=56.03;MQ0=0;MQRankSum=-2.863;QD=0.42;ReadPosRankSum=-0.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V99I|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:36,4:40:45:45,0,1148
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4477 chr1 174343 . C T 49.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.041;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=7.9983;MLEAC=1;MLEAF=0.500;MQ=56.35;MQ0=0;MQRankSum=-3.088;QD=1.11;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D94N|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:40,5:45:78:78,0,1238
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|
|
4478 chr1 174344 . A C 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.079;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=7.9983;MLEAC=1;MLEAF=0.500;MQ=56.47;MQ0=0;MQRankSum=3.308;QD=9.99;ReadPosRankSum=-2.122;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T93|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,16:45:99:478,0,949
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4479 chr1 174366 . A G 149.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-4.432;QD=2.63;ReadPosRankSum=-0.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L86P|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:48,9:57:99:178,0,1581
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4480 chr1 174384 . G A 218.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.258;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=12.0923;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=-4.975;QD=3.53;ReadPosRankSum=0.848;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P80L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:51,11:62:99:247,0,1745
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|
4481 chr1 174411 . C T 121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.558;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=17.8235;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-4.738;QD=2.14;ReadPosRankSum=1.981;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C71Y|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:48,9:57:99:150,0,1746
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4482 chr1 174419 . C T 104.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.538;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=17.8235;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-4.754;QD=1.78;ReadPosRankSum=1.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R68|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:50,9:59:99:133,0,1748
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|
4483 chr1 174420 . C T 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.019;DP=60;Dels=0.00;FS=1.030;HaplotypeScore=17.8235;MLEAC=1;MLEAF=0.500;MQ=58.46;MQ0=0;MQRankSum=2.493;QD=11.21;ReadPosRankSum=-0.030;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R68K|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:37,23:60:99:701,0,1219
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4484 chr1 174440 . G A 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.576;DP=60;Dels=0.00;FS=3.855;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=-4.283;QD=0.50;ReadPosRankSum=-0.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S61|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:53,7:60:58:58,0,1883
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4485 chr1 174476 . C T 1633.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.230;DP=51;Dels=0.00;FS=10.504;HaplotypeScore=2.3300;MLEAC=2;MLEAF=1.00;MQ=59.01;MQ0=0;MQRankSum=2.857;QD=32.03;ReadPosRankSum=-0.813;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S49|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:3,48:51:40:1662,40,0
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4486 chr1 174490 . C T 112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=53;Dels=0.00;FS=8.491;HaplotypeScore=2.3724;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-3.764;QD=2.13;ReadPosRankSum=-0.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D45N|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:45,8:53:99:141,0,1535
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4487 chr1 174501 . C T 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.101;DP=50;Dels=0.00;FS=5.507;HaplotypeScore=2.3724;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-3.283;QD=3.02;ReadPosRankSum=-0.808;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R41H|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:41,9:50:99:179,0,1448
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4488 chr1 174533 . C G 2385.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.9967;MLEAC=2;MLEAF=1.00;MQ=56.66;MQ0=0;QD=25.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L30|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2414,184,0
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4489 chr1 174565 . T C 210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.951;DP=66;Dels=0.00;FS=2.875;HaplotypeScore=1.6281;MLEAC=1;MLEAF=0.500;MQ=57.27;MQ0=0;MQRankSum=-1.776;QD=3.19;ReadPosRankSum=0.604;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T20A|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:54,11:66:99:239,0,1827
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4490 chr1 174590 . C A 69.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.835;DP=58;Dels=0.00;FS=6.430;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.01;MQ0=0;MQRankSum=-2.077;QD=1.20;ReadPosRankSum=-0.979;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L11F|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:51,7:58:98:98,0,1786
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4491 chr1 174616 . C T 904.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.798;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=3.4534;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-0.293;QD=18.46;ReadPosRankSum=0.434;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A3T|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:21,28:49:99:933,0,662
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4492 chr1 174675 . G A 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=42;Dels=0.00;FS=11.439;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.088;QD=15.57;ReadPosRankSum=0.869;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:682,0,737
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4493 chr1 174689 . G A 661.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.132;DP=47;Dels=0.00;FS=8.283;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.96;MQ0=0;MQRankSum=-0.221;QD=14.08;ReadPosRankSum=0.485;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,21:47:99:690,0,836
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4494 chr1 174766 . G A 164.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=25.9922;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=1;MQRankSum=2.107;QD=3.74;ReadPosRankSum=-1.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:36,8:44:99:193,0,1204
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4495 chr1 174767 . G A 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.047;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=25.9922;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=1;MQRankSum=-1.576;QD=3.65;ReadPosRankSum=-0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:36,8:44:99:189,0,1253
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4496 chr1 174776 . G T 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.083;DP=30;Dels=0.00;FS=12.809;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.31;MQ0=1;MQRankSum=-0.811;QD=17.13;ReadPosRankSum=0.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:542,0,441
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4497 chr1 174825 . T C 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.264;DP=30;Dels=0.00;FS=5.710;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-2.260;QD=18.79;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:592,0,412
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4498 chr1 174849 . C T 503.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=9.9864;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.85;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:532,39,0
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4499 chr1 174856 . T C 426.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.124;DP=31;Dels=0.00;FS=1.862;HaplotypeScore=9.9864;MLEAC=1;MLEAF=0.500;MQ=56.35;MQ0=1;MQRankSum=-3.069;QD=13.77;ReadPosRankSum=-2.821;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:455,0,505
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4500 chr1 174866 . G T 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.717;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=56.78;MQ0=1;MQRankSum=-2.467;QD=18.28;ReadPosRankSum=-2.747;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:14,21:35:99:668,0,443
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4501 chr1 174893 . G C 1410.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.79;MQ0=0;QD=27.44;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1439,108,0
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|
4502 chr1 174896 . A G 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.059;DP=36;Dels=0.00;FS=7.563;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-1.893;QD=18.63;ReadPosRankSum=2.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,21:36:99:699,0,483
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4503 chr1 174908 . G A 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.143;DP=36;Dels=0.00;FS=7.479;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=0.525;QD=14.19;ReadPosRankSum=-1.480;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:539,0,683
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|
4504 chr1 174931 . A T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.783;DP=33;Dels=0.00;FS=7.712;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-0.630;QD=15.27;ReadPosRankSum=0.486;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,16:33:99:532,0,597
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4505 chr1 174937 . T C 474.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.813;DP=33;Dels=0.00;FS=7.702;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-1.284;QD=14.39;ReadPosRankSum=0.524;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:503,0,630
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4506 chr1 174940 . C A 1210.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.94;MQ0=0;QD=29.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1239,93,0
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|
|
4507 chr1 174946 . T C 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.250;DP=35;Dels=0.00;FS=10.992;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-1.150;QD=13.19;ReadPosRankSum=0.150;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,15:35:99:490,0,676
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|
|
4508 chr1 174949 . A T 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.150;DP=37;Dels=0.00;FS=16.331;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=-0.751;QD=13.40;ReadPosRankSum=-0.291;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:524,0,731
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|
|
4509 chr1 174959 . A C 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.957;DP=36;Dels=0.00;FS=23.979;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.535;QD=11.58;ReadPosRankSum=0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:445,0,733
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|
|
4510 chr1 174960 . G C 1421.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=2;MLEAF=1.00;MQ=59.11;MQ0=0;QD=27.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1450,108,0
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|
|
4511 chr1 174965 . A G 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.564;DP=38;Dels=0.00;FS=25.258;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.777;QD=15.76;ReadPosRankSum=1.173;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,20:38:99:627,0,565
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|
|
4512 chr1 175000 . T C 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.494;DP=31;Dels=0.00;FS=19.167;HaplotypeScore=3.5778;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=1.048;QD=16.86;ReadPosRankSum=0.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:551,0,513
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|
|
4513 chr1 175050 . C T 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.635;DP=25;Dels=0.00;FS=1.685;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.01;MQ0=0;MQRankSum=-3.633;QD=11.15;ReadPosRankSum=2.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,10:25:99:307,0,488
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|
|
4514 chr1 175051 . G A 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.191;DP=25;Dels=0.00;FS=1.685;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.08;MQ0=0;MQRankSum=-4.077;QD=10.91;ReadPosRankSum=2.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,10:25:99:301,0,523
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|
|
4515 chr1 175057 . G A 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.016;DP=23;Dels=0.00;FS=1.713;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=-3.752;QD=12.08;ReadPosRankSum=1.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:306,0,446
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|
|
4516 chr1 175058 . T C 814.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.04;MQ0=0;QD=27.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,23:23:63:843,63,0
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|
|
4517 chr1 175059 . A G 366.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.796;DP=24;Dels=0.00;FS=3.741;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.91;MQ0=0;MQRankSum=3.766;QD=15.28;ReadPosRankSum=-1.622;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:11,13:24:99:395,0,347
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|
|
4518 chr1 175061 . C T 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.415;DP=26;Dels=0.00;FS=1.685;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.16;MQ0=0;MQRankSum=-3.944;QD=10.22;ReadPosRankSum=1.609;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,11:26:99:294,0,532
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|
|
4519 chr1 175067 . T C 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.392;DP=33;Dels=0.00;FS=1.428;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.56;MQ0=0;MQRankSum=4.465;QD=14.78;ReadPosRankSum=1.067;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:516,0,577
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|
|
4520 chr1 175070 . T C 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.850;DP=33;Dels=0.00;FS=1.428;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.56;MQ0=0;MQRankSum=-4.501;QD=17.05;ReadPosRankSum=-1.284;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,18:33:99:591,0,501
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|
|
4521 chr1 175078 . G T 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.051;DP=37;Dels=0.00;FS=1.331;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-4.709;QD=17.24;ReadPosRankSum=-1.021;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:666,0,570
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|
|
4522 chr1 175079 . G A 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.265;DP=37;Dels=0.00;FS=1.331;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-4.800;QD=17.35;ReadPosRankSum=-1.204;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:670,0,560
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|
|
4523 chr1 175082 . T C 545.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.533;DP=37;Dels=0.00;FS=1.331;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=4.587;QD=14.75;ReadPosRankSum=1.082;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:574,0,663
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|
|
4524 chr1 175088 . C T 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.728;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=0;MQRankSum=-4.931;QD=16.17;ReadPosRankSum=-0.267;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:659,0,646
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|
|
4525 chr1 175118 . A G 626.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.220;DP=33;Dels=0.00;FS=1.402;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.45;MQ0=0;MQRankSum=4.681;QD=18.99;ReadPosRankSum=-2.131;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:14,19:33:99:655,0,376
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|
|
4526 chr1 175131 . T C 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.927;DP=32;Dels=0.00;FS=1.440;HaplotypeScore=18.3970;MLEAC=1;MLEAF=0.500;MQ=54.29;MQ0=0;MQRankSum=-4.457;QD=11.06;ReadPosRankSum=1.226;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:382,0,689
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|
|
4527 chr1 175148 . T G 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.711;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=55.44;MQ0=0;MQRankSum=-2.725;QD=1.21;ReadPosRankSum=-0.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,3:18:50:50,0,556
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|
|
4528 chr1 175149 . T C 617.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=55.44;MQ0=0;QD=34.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,17:18:48:646,48,0
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|
|
4529 chr1 175157 . T C 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.168;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=1.9788;MLEAC=1;MLEAF=0.500;MQ=55.69;MQ0=0;MQRankSum=-2.739;QD=0.94;ReadPosRankSum=-1.174;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:16,3:19:46:46,0,572
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|
|
4530 chr1 175160 . C T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.509;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.69;MQ0=0;MQRankSum=-2.739;QD=0.78;ReadPosRankSum=-1.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:16,3:19:43:43,0,598
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|
|
4531 chr1 175191 . T C 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.635;DP=24;Dels=0.00;FS=2.644;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=-3.412;QD=1.41;ReadPosRankSum=-1.208;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:19,5:24:62:62,0,696
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|
|
4532 chr1 175195 . A G 669.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.355;DP=24;Dels=0.00;FS=2.682;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=3.341;QD=27.91;ReadPosRankSum=0.213;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:5,19:24:71:698,0,71
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|
|
4533 chr1 175196 . C T 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.932;DP=23;Dels=0.00;FS=2.671;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=-3.391;QD=1.90;ReadPosRankSum=-0.261;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,5:23:72:72,0,661
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|
|
4534 chr1 175215 . A C 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=26;Dels=0.00;FS=15.740;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.78;MQ0=0;MQRankSum=-4.028;QD=6.64;ReadPosRankSum=-0.028;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:201,0,652
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|
|
4535 chr1 175251 . C T 1564.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.50;MQ0=0;QD=35.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1593,117,0
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|
|
4536 chr1 175255 . C A 1746.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.74;MQ0=0;QD=28.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1775,132,0
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|
|
4537 chr1 175270 . T G 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.924;DP=54;Dels=0.00;FS=2.436;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=54.07;MQ0=0;MQRankSum=-5.061;QD=12.94;ReadPosRankSum=-0.484;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:727,0,1094
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|
|
4538 chr1 175316 . G A 645.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.625;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.26;MQ0=0;MQRankSum=-3.991;QD=13.74;ReadPosRankSum=1.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:674,0,909
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|
4539 chr1 175333 . A G 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.966;DP=41;Dels=0.00;FS=1.298;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.98;MQ0=0;MQRankSum=-4.353;QD=11.17;ReadPosRankSum=0.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:486,0,819
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|
|
4540 chr1 175342 . C T 387.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.626;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.71;MQ0=0;MQRankSum=-4.498;QD=9.69;ReadPosRankSum=0.475;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:416,0,840
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|
|
4541 chr1 175343 . A G 377.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.450;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.90;MQ0=0;MQRankSum=-4.561;QD=9.21;ReadPosRankSum=0.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:406,0,870
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|
|
4542 chr1 175351 . C T 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.893;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=53.10;MQ0=0;MQRankSum=-4.553;QD=8.76;ReadPosRankSum=-0.073;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:370,0,874
|
|
|
4543 chr1 175354 . T A 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.428;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.75;MQ0=0;MQRankSum=-4.347;QD=8.35;ReadPosRankSum=-0.626;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,13:36:99:329,0,790
|
|
|
4544 chr1 175364 . T A 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.351;DP=34;Dels=0.00;FS=1.879;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=53.40;MQ0=0;MQRankSum=-4.021;QD=4.35;ReadPosRankSum=-0.859;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,9:34:99:176,0,882
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|
|
4545 chr1 175395 . C T 1069.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.59;MQ0=0;QD=29.50;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,29:29:81:1098,81,0
|
|
|
4546 chr1 175462 . C T 381.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.111;DP=54;Dels=0.00;FS=9.949;HaplotypeScore=6.9505;MLEAC=1;MLEAF=0.500;MQ=51.04;MQ0=2;MQRankSum=-4.141;QD=7.07;ReadPosRankSum=-0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:39,15:54:99:410,0,1172
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|
4547 chr1 175465 . G A 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.799;DP=52;Dels=0.00;FS=7.479;HaplotypeScore=6.9505;MLEAC=1;MLEAF=0.500;MQ=50.66;MQ0=2;MQRankSum=-4.022;QD=7.53;ReadPosRankSum=-0.931;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:36,15:52:99:420,0,1104
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|
4548 chr1 175476 . A G 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.975;DP=49;Dels=0.00;FS=9.035;HaplotypeScore=4.6337;MLEAC=1;MLEAF=0.500;MQ=50.04;MQ0=2;MQRankSum=-4.277;QD=8.16;ReadPosRankSum=2.099;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:33,16:49:99:428,0,984
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|
4549 chr1 175478 . A G 424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.647;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=4.6337;MLEAC=1;MLEAF=0.500;MQ=50.04;MQ0=2;MQRankSum=-5.820;QD=8.67;ReadPosRankSum=4.142;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:453,0,901
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|
4550 chr1 175489 . G A 426.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.045;DP=42;Dels=0.00;FS=4.393;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=48.18;MQ0=2;MQRankSum=-3.213;QD=10.16;ReadPosRankSum=4.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:455,0,695
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|
4551 chr1 175502 . C T 373.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.769;DP=37;Dels=0.00;FS=3.650;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.65;MQ0=1;MQRankSum=-5.014;QD=10.10;ReadPosRankSum=3.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:402,0,770
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|
4552 chr1 175510 . G A 255.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.695;DP=29;Dels=0.00;FS=4.386;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.46;MQ0=1;MQRankSum=-4.339;QD=8.82;ReadPosRankSum=1.942;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:284,0,642
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|
4553 chr1 175518 . C T 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.414;DP=29;Dels=0.00;FS=2.032;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.46;MQ0=1;MQRankSum=4.291;QD=21.16;ReadPosRankSum=-0.791;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:11,18:29:99:642,0,280
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|
4554 chr1 175519 . T C 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.728;DP=26;Dels=0.00;FS=1.927;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.53;MQ0=1;MQRankSum=-3.990;QD=6.95;ReadPosRankSum=0.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:209,0,614
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4555 chr1 175550 . T C 868.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.84;MQ0=0;QD=29.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:897,69,0
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|
4556 chr1 175583 . C G 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.905;DP=43;Dels=0.00;FS=3.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.67;MQ0=0;MQRankSum=-4.384;QD=4.32;ReadPosRankSum=-4.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:32,11:43:99:214,0,1136
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4557 chr1 175588 . A T 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.168;DP=44;Dels=0.00;FS=1.379;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.85;MQ0=0;MQRankSum=-4.418;QD=4.88;ReadPosRankSum=-2.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:33,11:44:99:243,0,1139
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4558 chr1 175611 . A C 222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.250;DP=48;Dels=0.00;FS=1.311;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=52.65;MQ0=0;MQRankSum=-4.679;QD=4.64;ReadPosRankSum=1.869;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:36,12:48:99:251,0,1281
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4559 chr1 175625 . A C 1275.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.57;MQ0=0;QD=28.48;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1304,99,0
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4560 chr1 175674 . T C 812.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.22;MQ0=0;QD=33.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,23:23:63:841,63,0
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|
4561 chr1 175724 . C T 657.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.67;MQ0=0;QD=29.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:686,54,0
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|
4562 chr1 175730 . G A 621.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.11;MQ0=0;QD=31.41;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:650,51,0
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|
4563 chr1 175731 . A G 612.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.11;MQ0=0;QD=26.71;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:641,51,0
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4564 chr1 175771 . A G 825.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.18;MQ0=0;QD=25.43;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,21:22:63:854,63,0
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4565 chr1 175776 . G A 814.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.18;MQ0=0;QD=27.05;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:843,66,0
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4566 chr1 175784 . T C 738.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.94;MQ0=0;QD=33.97;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:767,57,0
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|
4567 chr1 175787 . G A 702.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.45;MQ0=0;QD=30.59;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:731,54,0
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|
4568 chr1 175809 . C T 591.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.30;MQ0=0;QD=29.59;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:620,45,0
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|
4569 chr1 175815 . G T 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.594;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.594;QD=0.74;ReadPosRankSum=2.123;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:13,2:15:39:39,0,491
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4570 chr1 175833 . C A 177.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.203;QD=19.75;ReadPosRankSum=-1.203;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:3,6:9:88:206,0,88
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4571 chr1 175887 . T A 491.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=31;Dels=0.00;FS=11.982;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=57.42;MQ0=1;MQRankSum=-0.104;QD=15.86;ReadPosRankSum=0.894;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:520,0,468
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4572 chr1 175892 . C T 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.327;DP=30;Dels=0.00;FS=11.831;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=0.240;QD=15.53;ReadPosRankSum=2.859;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,15:30:99:494,0,466
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4573 chr1 175895 . T A 442.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.807;DP=30;Dels=0.00;FS=8.557;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=-0.982;QD=14.76;ReadPosRankSum=2.990;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,15:30:99:471,0,475
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4574 chr1 175993 . C A 385.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.200;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.85;MQ0=0;MQRankSum=-0.646;QD=16.77;ReadPosRankSum=0.031;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,12:23:99:414,0,304
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4575 chr1 176009 . T C 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.368;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=53.56;MQ0=0;MQRankSum=0.380;QD=16.09;ReadPosRankSum=2.507;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:9,11:20:99:350,0,229
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4576 chr1 176036 . A T 405.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.485;DP=21;Dels=0.00;FS=4.419;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=0.187;QD=19.32;ReadPosRankSum=-1.604;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:7,14:21:99:434,0,213
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4577 chr1 176049 . C T 718.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=58.65;MQ0=0;QD=21.77;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:747,60,0
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4578 chr1 176097 . T G 339.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.98;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:368,30,0
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4579 chr1 176139 . C T 883.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.97;MQ0=0;QD=32.45;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:912,69,0
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4580 chr1 176158 . C G 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.870;DP=26;Dels=0.00;FS=24.095;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=1.397;QD=10.95;ReadPosRankSum=-0.079;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,10:26:99:313,0,559
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|
4581 chr1 176165 . T C 291.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.778;DP=27;Dels=0.00;FS=25.156;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=0.979;QD=10.81;ReadPosRankSum=-0.226;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,10:27:99:320,0,588
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|
4582 chr1 176174 . T C 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.318;DP=24;Dels=0.00;FS=23.395;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=0;MQRankSum=-0.381;QD=7.07;ReadPosRankSum=-0.064;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,7:24:99:198,0,602
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4583 chr1 176177 . G A 905.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.96;MQ0=0;QD=29.06;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,25:25:69:934,69,0
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|
|
4584 chr1 176195 . C T 1025.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.45;MQ0=0;QD=32.16;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1054,78,0
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|
|
4585 chr1 176207 . C T 870.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.28;MQ0=0;QD=26.36;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,24:24:66:899,66,0
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|
|
4586 chr1 176233 . C T 725.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.85;MQ0=0;QD=26.02;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:754,57,0
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|
|
4587 chr1 176286 . G A 535.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.55;MQ0=0;QD=31.52;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:45:564,45,0
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|
|
4588 chr1 176290 . A G 560.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=2;MLEAF=1.00;MQ=50.55;MQ0=0;QD=32.99;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:48:589,48,0
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|
|
4589 chr1 176293 . G A 373.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.510;DP=17;Dels=0.00;FS=6.117;HaplotypeScore=12.9225;MLEAC=1;MLEAF=0.500;MQ=49.38;MQ0=0;MQRankSum=1.642;QD=21.99;ReadPosRankSum=2.774;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:4,13:17:99:402,0,106
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|
|
4590 chr1 176307 . T A 463.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.868;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=15.9189;MLEAC=2;MLEAF=1.00;MQ=48.64;MQ0=0;MQRankSum=-1.519;QD=28.96;ReadPosRankSum=1.519;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:1,15:16:9:491,9,0
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|
|
4591 chr1 176308 . T A 420.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.556;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=15.9189;MLEAC=1;MLEAF=0.500;MQ=48.64;MQ0=0;MQRankSum=-2.302;QD=26.30;ReadPosRankSum=1.826;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:2,14:16:32:449,0,32
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|
|
4592 chr1 176309 . T A 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.031;DP=16;Dels=0.00;FS=6.317;HaplotypeScore=14.9199;MLEAC=1;MLEAF=0.500;MQ=48.64;MQ0=0;MQRankSum=-1.637;QD=5.24;ReadPosRankSum=0.667;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:12,4:16:99:112,0,330
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|
|
4593 chr1 176346 . T A 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.960;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=6.9981;MLEAC=1;MLEAF=0.500;MQ=49.11;MQ0=0;MQRankSum=-1.920;QD=5.44;ReadPosRankSum=-0.175;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,5:20:99:137,0,516
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|
|
4594 chr1 176350 . T C 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.440;DP=21;Dels=0.00;FS=7.501;HaplotypeScore=6.9981;MLEAC=1;MLEAF=0.500;MQ=49.68;MQ0=0;MQRankSum=0.662;QD=22.85;ReadPosRankSum=-0.117;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:6,15:21:99:508,0,178
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|
|
4595 chr1 176353 . T C 739.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=5.9978;MLEAC=2;MLEAF=1.00;MQ=49.68;MQ0=0;QD=24.14;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,20:21:60:768,60,0
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|
|
4596 chr1 176364 . G A 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.154;DP=30;Dels=0.00;FS=6.914;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=-0.110;QD=9.29;ReadPosRankSum=-0.374;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,10:30:99:307,0,694
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|
|
4597 chr1 176371 . A G 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.936;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.66;MQ0=0;MQRankSum=0.363;QD=9.24;ReadPosRankSum=-0.325;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,11:33:99:333,0,777
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|
4598 chr1 176377 . G A 1335.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.86;MQ0=0;QD=32.95;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1364,102,0
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|
|
4599 chr1 176389 . G C 1302.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.9993;MLEAC=2;MLEAF=1.00;MQ=55.23;MQ0=0;QD=22.29;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1331,99,0
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|
|
4600 chr1 176391 . A G 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.646;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=55.23;MQ0=0;MQRankSum=0.568;QD=8.05;ReadPosRankSum=-1.273;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,10:33:99:294,0,820
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|
|
4601 chr1 176394 . G A 276.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.255;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=55.23;MQ0=0;MQRankSum=0.333;QD=8.39;ReadPosRankSum=-0.842;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,10:33:99:305,0,820
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|
|
4602 chr1 176397 . C T 259.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.338;DP=32;Dels=0.00;FS=9.755;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=0;MQRankSum=0.427;QD=8.12;ReadPosRankSum=-1.037;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:288,0,782
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|
|
4603 chr1 176400 . G A 1117.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=1.9993;MLEAC=2;MLEAF=1.00;MQ=56.80;MQ0=0;QD=27.50;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,30:30:87:1146,87,0
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|
|
4604 chr1 176402 . T A 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.647;DP=34;Dels=0.00;FS=11.168;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=57.36;MQ0=0;MQRankSum=0.472;QD=19.23;ReadPosRankSum=0.332;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,20:34:99:682,0,440
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|
|
4605 chr1 176422 . C T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.143;DP=43;Dels=0.00;FS=10.456;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=-0.013;QD=10.02;ReadPosRankSum=0.716;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,16:43:99:459,0,874
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|
4606 chr1 176432 . G T 846.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.659;DP=44;Dels=0.00;FS=10.793;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.275;QD=19.24;ReadPosRankSum=-0.131;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,26:44:99:875,0,599
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|
4607 chr1 176471 . G C 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.307;DP=39;Dels=0.00;FS=2.886;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.520;QD=15.99;ReadPosRankSum=-0.239;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:652,0,620
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|
4608 chr1 176483 . T G 746.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.208;DP=46;Dels=0.00;FS=2.660;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.714;QD=16.23;ReadPosRankSum=-0.022;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:775,0,731
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|
4609 chr1 176494 . G A 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.467;DP=44;Dels=0.00;FS=4.658;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.705;QD=17.68;ReadPosRankSum=1.292;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:806,0,667
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|
4610 chr1 176561 . T C 1205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.346;DP=45;Dels=0.00;FS=7.565;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.578;QD=26.79;ReadPosRankSum=-1.424;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:12,33:45:99:1234,0,358
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|
4611 chr1 176568 . G C 285.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.949;DP=44;Dels=0.00;FS=5.029;HaplotypeScore=20.3301;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.488;QD=6.49;ReadPosRankSum=1.464;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:33,11:44:99:314,0,1180
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|
4612 chr1 176599 . G C 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.485;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.076;QD=0.94;ReadPosRankSum=-0.227;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:32,4:37:63:63,0,1130
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|
4613 chr1 176618 . C T 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.231;DP=49;Dels=0.00;FS=1.114;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.553;QD=14.46;ReadPosRankSum=-2.864;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:737,0,944
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|
4614 chr1 176635 . C T 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.787;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.075;QD=13.67;ReadPosRankSum=1.784;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:26,20:46:99:657,0,863
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|
4615 chr1 176661 . A T 1847.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.95;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1876,141,0
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|
4616 chr1 176688 . T C 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.618;DP=44;Dels=0.00;FS=5.897;HaplotypeScore=0.9332;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=1;MQRankSum=-0.962;QD=18.13;ReadPosRankSum=0.110;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:826,0,625
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|
4617 chr1 176698 . C T 1695.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=2;MLEAF=1.00;MQ=57.62;MQ0=1;QD=32.63;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1724,129,0
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|
4618 chr1 176733 . G A 903.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.44;MQ0=1;QD=32.93;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,24:24:69:932,69,0
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|
4619 chr1 176761 . A T 38.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.205;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.97;MQ0=1;MQRankSum=1.449;QD=2.15;ReadPosRankSum=-2.457;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,3:18:67:67,0,485
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4620 chr1 176800 . G A 390.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.42;MQ0=0;QD=30.63;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:419,33,0
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|
4621 chr1 176848 . G T 11.83 LowQual AC=2;AF=1.00;AN=2;BaseQRankSum=0.804;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.90;MQ0=0;MQRankSum=0.804;QD=5.91;ReadPosRankSum=0.804;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:1,1:2:3:38,3,0
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|
4622 chr1 177059 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.067;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=12.03;MQ0=24;MQRankSum=-1.333;QD=1.47;ReadPosRankSum=2.933;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,11:38:84:84,0,91
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|
4623 chr1 177070 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.788;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=11.58;MQ0=27;MQRankSum=-0.689;QD=1.43;ReadPosRankSum=-2.793;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:29,9:39:84:84,0,91
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|
4624 chr1 177088 . A C 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.599;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=10.40;MQ0=30;MQRankSum=0.825;QD=0.71;ReadPosRankSum=-0.600;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:36,6:42:58:58,0,94
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|
4625 chr1 177252 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.667;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=10.59;MQ0=35;MQRankSum=-1.333;QD=1.14;ReadPosRankSum=-1.867;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:36,13:49:84:84,0,91
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|
|
4626 chr1 177401 . A C 299.78 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.64;MQ0=0;QD=18.74;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,16:16:24:328,24,0
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|
|
4627 chr1 177522 . A C 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.083;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.77;MQ0=0;MQRankSum=-1.692;QD=19.39;ReadPosRankSum=-0.971;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:10,15:25:99:513,0,327
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|
|
4628 chr1 177533 . A C 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.661;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=0;MQRankSum=-1.713;QD=17.07;ReadPosRankSum=-0.415;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,15:26:99:472,0,360
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|
|
4629 chr1 177599 . C T 1453.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.74;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1482,111,0
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|
|
4630 chr1 177668 . A G 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.681;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-0.893;QD=10.57;ReadPosRankSum=0.741;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:430,0,785
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|
|
4631 chr1 177672 . C G 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.827;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=-0.730;QD=11.08;ReadPosRankSum=0.438;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:427,0,755
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|
|
4632 chr1 177673 . T C 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.730;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=-0.990;QD=11.33;ReadPosRankSum=0.406;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:436,0,759
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|
|
4633 chr1 177685 . C T 1270.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=40.5933;MLEAC=2;MLEAF=1.00;MQ=57.82;MQ0=0;QD=30.38;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1299,96,0
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|
|
4634 chr1 177713 . T C 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.250;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.12;MQ0=0;MQRankSum=4.183;QD=19.34;ReadPosRankSum=0.383;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:705,0,508
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|
|
4635 chr1 177736 . T G 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.22;MQ0=0;MQRankSum=-4.078;QD=12.81;ReadPosRankSum=0.906;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,15:32:99:438,0,601
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|
|
4636 chr1 177753 . T A 1468.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.25;MQ0=0;QD=28.29;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1497,114,0
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|
|
4637 chr1 177771 . C T 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.095;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.27;MQ0=0;MQRankSum=-4.477;QD=16.37;ReadPosRankSum=0.663;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:683,0,691
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|
|
4638 chr1 177787 . T C 1629.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=56.90;MQ0=0;QD=33.13;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1658,123,0
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|
|
4639 chr1 177789 . A G 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.560;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.25;MQ0=0;MQRankSum=4.009;QD=13.47;ReadPosRankSum=1.245;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,20:46:99:648,0,869
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|
|
4640 chr1 177795 . G T 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.622;DP=44;Dels=0.00;FS=1.177;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=-1.983;QD=16.77;ReadPosRankSum=-0.270;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:766,0,709
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|
|
4641 chr1 177797 . C T 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.081;DP=43;Dels=0.00;FS=1.177;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.23;MQ0=0;MQRankSum=-2.636;QD=17.06;ReadPosRankSum=-0.595;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:762,0,706
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|
|
4642 chr1 177814 . C T 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.198;DP=44;Dels=0.00;FS=2.498;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=58.25;MQ0=0;MQRankSum=-2.138;QD=16.18;ReadPosRankSum=-0.047;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:740,0,797
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|
4643 chr1 177863 . C A 826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.327;DP=44;Dels=0.00;FS=2.649;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-0.900;QD=18.79;ReadPosRankSum=0.237;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:855,0,637
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|
|
4644 chr1 177874 . C T 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.014;DP=46;Dels=0.00;FS=2.569;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.816;QD=14.93;ReadPosRankSum=-0.860;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,21:46:99:715,0,849
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|
4645 chr1 177924 . T G 554.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.175;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.467;QD=14.22;ReadPosRankSum=0.014;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:583,0,741
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4646 chr1 177937 . A G 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.034;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=1.402;QD=13.92;ReadPosRankSum=-1.034;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:571,0,787
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|
4647 chr1 177938 . T C 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.869;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=0.327;QD=14.73;ReadPosRankSum=-1.556;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:632,0,783
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|
4648 chr1 177940 . C T 783.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.961;DP=44;Dels=0.00;FS=2.498;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-1.786;QD=17.81;ReadPosRankSum=1.645;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:812,0,687
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|
4649 chr1 177955 . T C 962.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.952;DP=48;Dels=0.00;FS=1.129;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=1.014;QD=20.06;ReadPosRankSum=0.178;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,28:48:99:991,0,659
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4650 chr1 177959 . T G 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.975;DP=49;Dels=0.00;FS=1.137;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-0.359;QD=12.16;ReadPosRankSum=0.544;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:624,0,1063
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|
4651 chr1 177983 . A G 1899.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=2.4892;MLEAC=2;MLEAF=1.00;MQ=59.77;MQ0=0;QD=26.52;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1928,144,0
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|
|
4652 chr1 177992 . G A 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.582;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.388;QD=17.00;ReadPosRankSum=0.466;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:878,0,780
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|
4653 chr1 178064 . C T 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.594;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.137;QD=14.80;ReadPosRankSum=-0.229;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:576,0,654
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|
4654 chr1 178089 . G C 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.777;DP=34;Dels=0.00;FS=3.270;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=1;MQRankSum=-0.777;QD=17.73;ReadPosRankSum=0.235;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,19:34:99:631,0,457
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|
4655 chr1 178121 . C A 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.759;DP=41;Dels=0.00;FS=1.294;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=1;MQRankSum=-1.035;QD=19.46;ReadPosRankSum=0.676;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,25:41:99:826,0,488
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|
4656 chr1 178255 . T C 358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.918;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.153;QD=11.21;ReadPosRankSum=1.458;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,13:32:99:387,0,613
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|
4657 chr1 178259 . T C 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.469;DP=29;Dels=0.00;FS=1.449;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.329;QD=13.89;ReadPosRankSum=1.206;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,13:29:99:431,0,537
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|
4658 chr1 178261 . T A 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.066;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.460;QD=12.41;ReadPosRankSum=1.250;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,13:29:99:388,0,533
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|
|
4659 chr1 178263 . T C 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.963;DP=30;Dels=0.00;FS=1.484;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.879;QD=13.29;ReadPosRankSum=1.549;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,13:30:99:427,0,582
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|
|
4660 chr1 178287 . G A 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.739;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.465;QD=12.47;ReadPosRankSum=-0.575;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,11:25:99:340,0,480
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|
|
4661 chr1 178289 . G C 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.381;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.205;QD=11.87;ReadPosRankSum=-0.263;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:313,0,481
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|
|
4662 chr1 178299 . A T 262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.271;DP=23;Dels=0.00;FS=1.674;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.403;QD=11.42;ReadPosRankSum=-0.465;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:291,0,437
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|
4663 chr1 178322 . G A 377.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.414;DP=26;Dels=0.00;FS=5.734;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.723;QD=14.53;ReadPosRankSum=-0.283;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,12:26:99:406,0,467
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|
|
4664 chr1 178360 . A G 519.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.944;DP=39;Dels=0.00;FS=9.536;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-1.169;QD=13.33;ReadPosRankSum=0.070;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:548,0,674
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|
|
4665 chr1 178364 . T A 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.080;DP=42;Dels=0.00;FS=6.822;HaplotypeScore=1.9946;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.639;QD=13.02;ReadPosRankSum=0.928;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:575,0,786
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|
|
4666 chr1 178390 . A G 1140.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=43.1047;MLEAC=2;MLEAF=1.00;MQ=58.29;MQ0=0;QD=36.62;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1169,87,0
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|
|
4667 chr1 178393 . A G 1175.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=32.4731;MLEAC=2;MLEAF=1.00;MQ=58.19;MQ0=0;QD=34.88;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1204,90,0
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|
|
4668 chr1 178400 . G A 1180.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.3670;MLEAC=2;MLEAF=1.00;MQ=57.96;MQ0=0;QD=26.43;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1209,93,0
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|
|
4669 chr1 178402 . A C 1294.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.3670;MLEAC=2;MLEAF=1.00;MQ=58.02;MQ0=0;QD=27.35;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1323,99,0
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|
|
4670 chr1 178406 . A G 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=37;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=3.905;QD=16.45;ReadPosRankSum=0.228;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,19:37:99:637,0,616
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|
|
4671 chr1 178418 . C T 1535.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.98;MQ0=0;QD=29.23;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1564,117,0
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|
|
4672 chr1 178431 . A G 1627.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.75;MQ0=0;QD=31.86;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1656,123,0
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|
|
4673 chr1 178470 . C T 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.086;DP=34;Dels=0.00;FS=2.928;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=-2.467;QD=17.46;ReadPosRankSum=-1.570;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:622,0,545
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|
|
4674 chr1 178476 . G T 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.612;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=57.56;MQ0=0;MQRankSum=-2.884;QD=8.63;ReadPosRankSum=1.078;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:244,0,611
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|
|
4675 chr1 178477 . A G 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.269;DP=26;Dels=0.00;FS=1.596;HaplotypeScore=1.9951;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-2.910;QD=9.80;ReadPosRankSum=0.701;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,9:26:99:283,0,607
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|
|
4676 chr1 178478 . C T 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.777;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=1.9951;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-3.466;QD=8.11;ReadPosRankSum=1.311;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:231,0,607
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|
|
4677 chr1 178481 . A G 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.087;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-3.408;QD=8.63;ReadPosRankSum=1.486;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:244,0,606
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|
|
4678 chr1 178485 . T C 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.141;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=1.9989;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-2.540;QD=11.53;ReadPosRankSum=0.329;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,11:28:99:351,0,575
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|
|
4679 chr1 178493 . T C 366.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-2.900;QD=12.23;ReadPosRankSum=1.207;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:395,0,593
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|
|
4680 chr1 178499 . T C 366.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.953;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-1.630;QD=12.23;ReadPosRankSum=1.503;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:395,0,603
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|
|
4681 chr1 178504 . A G 368.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.255;DP=28;Dels=0.00;FS=1.527;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-2.019;QD=13.17;ReadPosRankSum=0.998;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:397,0,533
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|
4682 chr1 178548 . T C 289.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.026;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-2.451;QD=11.14;ReadPosRankSum=-0.975;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,10:26:99:318,0,550
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|
4683 chr1 178628 . A G 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.831;DP=38;Dels=0.00;FS=1.378;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=0;MQRankSum=-1.015;QD=9.68;ReadPosRankSum=0.708;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,13:38:99:396,0,801
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|
4684 chr1 178641 . T C 1162.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=44.07;MQ0=0;QD=31.81;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,33:33:93:1191,93,0
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|
4685 chr1 178645 . G T 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.239;DP=31;Dels=0.00;FS=1.525;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.35;MQ0=0;MQRankSum=-0.152;QD=7.54;ReadPosRankSum=-0.457;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,9:31:99:262,0,672
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|
4686 chr1 178672 . T C 271.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.82;MQ0=0;QD=27.18;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,10:10:24:300,24,0
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|
4687 chr1 178673 . T C 269.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.82;MQ0=0;QD=26.98;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,10:10:24:298,24,0
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|
4688 chr1 178709 . G A 304.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.04;MQ0=3;QD=19.05;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,16:16:30:333,30,0
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|
4689 chr1 178719 . T C 176.84 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.41;MQ0=3;QD=14.74;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,12:12:18:205,18,0
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|
4690 chr1 178740 . C T 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.796;DP=26;Dels=0.00;FS=6.166;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=24.19;MQ0=11;MQRankSum=-1.408;QD=1.41;ReadPosRankSum=-0.674;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,8:26:65:65,0,324
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|
4691 chr1 178796 . T C 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.153;DP=25;Dels=0.00;FS=6.726;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=33.15;MQ0=9;MQRankSum=0.404;QD=2.11;ReadPosRankSum=2.153;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,10:25:81:81,0,383
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|
4692 chr1 178979 . T C 232.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.041;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=-0.286;QD=12.25;ReadPosRankSum=-0.041;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:10,9:19:99:261,0,334
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|
4693 chr1 179063 . T A 690.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=35.16;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:719,54,0
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|
4694 chr1 179198 . A G 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.885;DP=40;Dels=0.00;FS=9.838;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.25;MQ0=3;MQRankSum=4.522;QD=12.94;ReadPosRankSum=2.437;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,16:40:99:546,0,642
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|
4695 chr1 179200 . A T 1439.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.25;MQ0=3;QD=28.36;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1468,108,0
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|
4696 chr1 179320 . C T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=48;Dels=0.00;FS=4.336;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=-0.475;QD=15.77;ReadPosRankSum=0.578;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:785,0,835
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|
4697 chr1 179364 . T G 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.428;DP=58;Dels=0.00;FS=7.156;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=1.284;QD=17.29;ReadPosRankSum=0.801;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1031,0,933
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4698 chr1 179397 . G T 2003.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.90;MQ0=0;QD=29.19;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:2032,147,0
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|
4699 chr1 179511 . C T 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.212;DP=55;Dels=0.00;FS=1.064;HaplotypeScore=11.7849;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=1.179;QD=14.23;ReadPosRankSum=1.655;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:31,24:55:99:811,0,1053
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|
4700 chr1 179518 . C T 289.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.344;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=11.7849;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=0.855;QD=5.68;ReadPosRankSum=-0.078;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:39,12:51:99:318,0,1406
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|
4701 chr1 179542 . C T 332.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.582;DP=59;Dels=0.00;FS=2.644;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.05;MQ0=0;MQRankSum=2.112;QD=5.64;ReadPosRankSum=-0.814;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:46,13:59:99:361,0,1612
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|
|
4702 chr1 179564 . C T 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.408;DP=67;Dels=0.00;FS=6.477;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=54.15;MQ0=0;MQRankSum=-3.831;QD=16.70;ReadPosRankSum=-0.332;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:33,34:67:99:1147,0,1135
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|
4703 chr1 179583 . T C 2571.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=52.03;MQ0=0;QD=33.16;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2600,193,0
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|
|
4704 chr1 179617 . A T 2299.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.562;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.19;MQ0=0;MQRankSum=1.392;QD=28.69;ReadPosRankSum=0.085;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:1,60:61:99:2328,144,0
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|
4705 chr1 179762 . G A 933.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.767;DP=51;Dels=0.00;FS=1.114;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.21;MQ0=0;MQRankSum=-1.618;QD=18.31;ReadPosRankSum=-0.407;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:962,0,770
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|
|
4706 chr1 179884 . G C 308.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.415;DP=28;Dels=0.00;FS=4.028;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.47;MQ0=0;MQRankSum=-1.658;QD=11.03;ReadPosRankSum=0.184;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,13:28:99:337,0,516
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|
4707 chr1 179951 . C T 550.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.506;DP=48;Dels=0.00;FS=2.471;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=61.42;MQ0=0;MQRankSum=-2.488;QD=11.47;ReadPosRankSum=-0.021;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:29,19:48:99:579,0,987
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|
4708 chr1 180063 . G T 1117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.357;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.238;QD=18.63;ReadPosRankSum=-0.015;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,33:60:99:1146,0,891
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|
|
4709 chr1 180136 . T A 725.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.280;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-2.350;QD=16.88;ReadPosRankSum=-0.012;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:754,0,646
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|
|
4710 chr1 180164 . C T 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.143;DP=47;Dels=0.00;FS=2.546;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.075;QD=14.02;ReadPosRankSum=1.546;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:687,0,853
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|
4711 chr1 180372 . A C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.314;DP=38;Dels=0.00;FS=4.887;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.28;MQ0=0;MQRankSum=-1.285;QD=16.26;ReadPosRankSum=0.671;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:646,0,633
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|
4712 chr1 180419 . G T 1311.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=8.9974;MLEAC=2;MLEAF=1.00;MQ=58.26;MQ0=0;QD=32.14;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1340,102,0
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|
4713 chr1 180460 . G A 1379.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=2;MLEAF=1.00;MQ=57.15;MQ0=1;QD=29.16;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1408,105,0
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|
4714 chr1 180463 . T A 537.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.550;DP=35;Dels=0.00;FS=1.423;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=1;MQRankSum=2.273;QD=15.36;ReadPosRankSum=-0.517;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:566,0,578
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|
4715 chr1 180470 . G C 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.224;DP=36;Dels=0.00;FS=1.373;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=1;MQRankSum=3.571;QD=16.24;ReadPosRankSum=-1.604;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,18:36:99:613,0,506
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|
4716 chr1 180531 . A C 550.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.306;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=1;MQRankSum=0.486;QD=16.20;ReadPosRankSum=-0.847;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:579,0,522
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|
4717 chr1 180557 . C G 1180.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.08;MQ0=1;QD=32.27;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,32:32:90:1209,90,0
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|
4718 chr1 180708 . G A 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.318;DP=24;Dels=0.00;FS=4.269;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.223;QD=24.12;ReadPosRankSum=0.953;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S43N|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 0/1:7,17:24:99:607,0,206
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|
4719 chr1 180728 . A G 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.774;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-0.437;QD=9.58;ReadPosRankSum=-0.489;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R50G|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 0/1:18,9:27:99:287,0,626
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|
4720 chr1 180746 . C T 1097.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;QD=31.29;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P56S|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1126,90,0
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|
|
4721 chr1 180749 . T C 1103.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;QD=26.57;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C57R|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1132,87,0
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|
4722 chr1 180758 . C T 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;DP=25;Dels=0.00;FS=13.757;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=-0.027;QD=12.87;ReadPosRankSum=1.068;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L60F|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 0/1:14,11:25:99:350,0,458
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4723 chr1 181012 . A G 667.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.249;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.6617;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.626;QD=23.03;ReadPosRankSum=-0.542;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:9,20:29:99:696,0,216
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|
4724 chr1 181024 . C A 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.337;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.9989;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.742;QD=20.41;ReadPosRankSum=1.506;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,18:29:99:620,0,319
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|
4725 chr1 181102 . T G 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.886;DP=33;Dels=0.00;FS=3.837;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.862;QD=17.27;ReadPosRankSum=0.560;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,18:33:99:598,0,487
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|
4726 chr1 181156 . G A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.099;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=0.560;QD=12.49;ReadPosRankSum=-0.429;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:12,10:22:99:303,0,376
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|
4727 chr1 181173 . A C 171.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.766;DP=15;Dels=0.00;FS=3.256;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.59;MQ0=0;MQRankSum=0.884;QD=11.45;ReadPosRankSum=-0.648;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:9,6:15:99:200,0,268
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|
4728 chr1 181194 . A G 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.535;DP=19;Dels=0.00;FS=2.017;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=2.149;QD=7.51;ReadPosRankSum=-2.850;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:13,6:19:99:171,0,426
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4729 chr1 181230 . T A 1286.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.67;MQ0=0;QD=31.97;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1315,96,0
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4730 chr1 181244 . G T 1304.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.89;MQ0=0;QD=27.50;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1333,99,0
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4731 chr1 181276 . T C 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.427;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.632;QD=11.19;ReadPosRankSum=-0.905;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,13:36:99:431,0,793
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4732 chr1 181325 . G C 210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.452;DP=23;Dels=0.00;FS=2.299;HaplotypeScore=1.8279;MLEAC=1;MLEAF=0.500;MQ=56.80;MQ0=0;MQRankSum=-1.711;QD=9.16;ReadPosRankSum=0.678;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:239,0,509
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4733 chr1 181330 . A G 904.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=1.8279;MLEAC=2;MLEAF=1.00;MQ=56.57;MQ0=0;QD=31.12;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,24:24:72:933,72,0
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4734 chr1 181337 . A G 906.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=56.47;MQ0=0;QD=29.13;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:935,72,0
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4735 chr1 181340 . G A 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.025;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=1.5661;MLEAC=1;MLEAF=0.500;MQ=56.31;MQ0=0;MQRankSum=-1.259;QD=11.87;ReadPosRankSum=-0.205;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:313,0,471
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|
4736 chr1 181363 . C T 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.002;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-2.743;QD=9.21;ReadPosRankSum=0.936;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:240,0,515
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|
4737 chr1 181373 . C G 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.033;DP=23;Dels=0.00;FS=3.982;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-2.033;QD=8.99;ReadPosRankSum=0.484;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:235,0,521
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4738 chr1 181378 . A G 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.646;DP=23;Dels=0.00;FS=4.200;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.88;MQ0=0;MQRankSum=3.647;QD=19.64;ReadPosRankSum=-1.130;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:480,0,235
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4739 chr1 181389 . T G 653.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.19;MQ0=0;QD=30.52;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:682,54,0
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4740 chr1 181394 . T C 708.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=29.42;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:737,57,0
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4741 chr1 181400 . T C 686.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.03;MQ0=0;QD=29.72;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:715,54,0
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4742 chr1 181432 . C T 663.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.63;MQ0=0;QD=28.65;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:692,51,0
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4743 chr1 181520 . C T 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.692;DP=35;Dels=0.00;FS=3.290;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.29;MQ0=2;MQRankSum=-3.125;QD=7.62;ReadPosRankSum=1.141;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,14:35:99:295,0,721
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4744 chr1 181569 . C T 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.437;DP=41;Dels=0.00;FS=11.992;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=54.50;MQ0=0;MQRankSum=-0.807;QD=11.26;ReadPosRankSum=0.463;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:490,0,840
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4745 chr1 181583 . T C 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.827;DP=39;Dels=0.00;FS=8.484;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=-1.317;QD=12.25;ReadPosRankSum=1.827;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:506,0,762
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4746 chr1 181595 . G A 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.137;DP=37;Dels=0.00;FS=9.049;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=-1.322;QD=14.13;ReadPosRankSum=0.319;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:551,0,655
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4747 chr1 181616 . A G 1243.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.37;MQ0=0;QD=26.17;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,34:34:96:1272,96,0
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4748 chr1 181649 . A G 871.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.28;MQ0=0;QD=28.35;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,24:24:72:900,72,0
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4749 chr1 181678 . C A 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.180;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=11.4067;MLEAC=1;MLEAF=0.500;MQ=54.06;MQ0=0;MQRankSum=-0.467;QD=4.27;ReadPosRankSum=2.335;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,3:14:88:88,0,315
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4750 chr1 181750 . T C 1735.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.6208;MLEAC=2;MLEAF=1.00;MQ=61.04;MQ0=0;QD=29.40;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L98S|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1764,132,0
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4751 chr1 181932 . T C 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.890;DP=42;Dels=0.00;FS=2.883;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.09;MQ0=0;MQRankSum=-0.630;QD=20.26;ReadPosRankSum=0.577;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C159R|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:15,27:42:99:879,0,440
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|
|
4752 chr1 182026 . T G 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.046;DP=37;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=1.966;QD=13.51;ReadPosRankSum=0.625;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cGc|L190R|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:20,17:37:99:528,0,608
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|
4753 chr1 182058 . G C 1193.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=58.19;MQ0=0;QD=29.48;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Cta|V201L|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 1/1:0,33:33:93:1222,93,0
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|
4754 chr1 182100 . A G 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.141;DP=37;Dels=0.00;FS=16.118;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.13;MQ0=0;MQRankSum=2.302;QD=20.29;ReadPosRankSum=-0.955;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R215G|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:14,23:37:99:779,0,366
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|
4755 chr1 182108 . G A 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=39;Dels=0.00;FS=10.673;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-0.794;QD=9.92;ReadPosRankSum=0.188;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S217|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:24,15:39:99:415,0,775
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|
|
4756 chr1 182195 . C A 1439.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=59.85;MQ0=0;QD=30.91;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atA|I246|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1468,111,0
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|
|
4757 chr1 182198 . G A 616.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.546;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.182;QD=17.62;ReadPosRankSum=0.348;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L247|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:16,19:35:99:645,0,523
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|
4758 chr1 182199 . A T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.109;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.475;QD=17.35;ReadPosRankSum=0.792;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Ttg|M248L|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:17,19:36:99:653,0,531
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|
4759 chr1 182231 . G A 1226.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.83;MQ0=0;QD=29.57;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A258|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 1/1:0,33:33:96:1255,96,0
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|
4760 chr1 182291 . A G 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.930;DP=43;Dels=0.00;FS=26.079;HaplotypeScore=1.6650;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.032;QD=9.86;ReadPosRankSum=-0.828;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V278|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:28,15:43:99:452,0,940
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|
4761 chr1 182317 . C T 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.746;DP=43;Dels=0.00;FS=22.687;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=-0.239;QD=11.09;ReadPosRankSum=1.018;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,16:43:99:505,0,912
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|
|
4762 chr1 182395 . C T 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.875;DP=36;Dels=0.00;FS=3.014;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=0;MQRankSum=0.462;QD=13.88;ReadPosRankSum=-2.786;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:528,0,655
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|
4763 chr1 182404 . G A 717.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=42;Dels=0.00;FS=1.218;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.53;MQ0=0;MQRankSum=0.834;QD=17.09;ReadPosRankSum=0.430;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),SPLICE_SITE_ACCEPTOR(HIGH||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:746,0,627
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|
4764 chr1 182424 . G A 837.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.760;DP=47;Dels=0.00;FS=1.150;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=0.738;QD=17.82;ReadPosRankSum=0.952;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A287|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182405_182607) GT:AD:DP:GQ:PL 0/1:21,26:47:99:866,0,703
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|
4765 chr1 182545 . G A 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.911;DP=38;Dels=0.00;FS=1.257;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=0.986;QD=11.26;ReadPosRankSum=-1.015;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V328I|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182405_182607) GT:AD:DP:GQ:PL 0/1:23,15:38:99:456,0,764
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|
|
4766 chr1 182610 . A G 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.208;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.70;MQ0=0;MQRankSum=-2.012;QD=10.40;ReadPosRankSum=1.873;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,15:34:99:382,0,506
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|
4767 chr1 182637 . T C 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.289;DP=36;Dels=0.00;FS=8.730;HaplotypeScore=2.3122;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=0;MQRankSum=-2.372;QD=17.99;ReadPosRankSum=1.735;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,20:36:99:676,0,448
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|
4768 chr1 182641 . T C 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.109;DP=38;Dels=0.00;FS=13.898;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=56.24;MQ0=0;MQRankSum=-2.511;QD=14.86;ReadPosRankSum=2.365;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:593,0,579
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|
4769 chr1 182646 . A G,T 974.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.03;MQ0=0;QD=27.06;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/2:0,18,18:36:99:1162,642,594,520,0,465
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|
4770 chr1 182648 . A T 536.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.525;DP=35;Dels=0.00;FS=17.460;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.91;MQ0=0;MQRankSum=-2.723;QD=15.34;ReadPosRankSum=2.228;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:565,0,436
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|
|
4771 chr1 182657 . T C 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;DP=46;Dels=0.00;FS=7.638;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=-3.778;QD=18.06;ReadPosRankSum=-1.934;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,29:46:99:859,0,438
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|
4772 chr1 182668 . T C 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.640;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=5.9516;MLEAC=1;MLEAF=0.500;MQ=54.15;MQ0=0;MQRankSum=-3.805;QD=14.92;ReadPosRankSum=-0.685;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,31:50:99:774,0,262
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|
4773 chr1 182674 . A T 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.564;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=30.8083;MLEAC=1;MLEAF=0.500;MQ=54.48;MQ0=0;MQRankSum=-4.923;QD=15.46;ReadPosRankSum=-1.147;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,27:47:99:755,0,282
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|
4774 chr1 182714 . G A 2208.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=18.3637;MLEAC=2;MLEAF=1.00;MQ=56.43;MQ0=0;QD=25.68;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2237,172,0
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4775 chr1 182756 . A G 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=40;Dels=0.00;FS=6.474;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-0.783;QD=5.17;ReadPosRankSum=0.817;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:30,9:40:99:235,0,1016
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|
4776 chr1 182758 . G A 226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.359;DP=40;Dels=0.00;FS=9.072;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-1.078;QD=5.67;ReadPosRankSum=0.672;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:30,10:40:99:255,0,986
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|
4777 chr1 182775 . T G 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.370;DP=44;Dels=0.00;FS=3.185;HaplotypeScore=2.9961;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.227;QD=11.61;ReadPosRankSum=-2.232;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:539,0,817
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|
4778 chr1 182800 . A T 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.456;DP=41;Dels=0.00;FS=1.435;HaplotypeScore=1.6650;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=1.552;QD=14.73;ReadPosRankSum=0.039;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:632,0,657
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|
4779 chr1 182818 . G T 536.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.524;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-1.464;QD=16.27;ReadPosRankSum=1.320;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A353S|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:15,18:33:99:565,0,472
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|
4780 chr1 182821 . T G 524.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.271;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.4440;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-1.284;QD=15.90;ReadPosRankSum=1.392;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S354A|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:15,18:33:99:553,0,504
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|
4781 chr1 182977 . A G 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=61;Dels=0.00;FS=1.012;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.470;QD=13.67;ReadPosRankSum=1.411;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I406V|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:33,28:61:99:862,0,1096
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|
4782 chr1 183001 . T C 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.024;DP=56;Dels=0.00;FS=2.198;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=1.958;QD=15.73;ReadPosRankSum=0.156;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L414|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:28,28:56:99:909,0,927
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|
4783 chr1 183099 . A G 694.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.275;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-1.462;QD=15.10;ReadPosRankSum=-1.154;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L446|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,24:46:99:723,0,679
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4784 chr1 183112 . A T 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.800;DP=47;Dels=0.00;FS=2.546;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-1.631;QD=13.93;ReadPosRankSum=-1.738;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Tgt|S451C|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:683,0,847
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4785 chr1 183122 . A G 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.754;DP=49;Dels=0.00;FS=6.090;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=-0.010;QD=14.34;ReadPosRankSum=-1.538;EFF=SYNONYMOUS_STOP(LOW|SILENT|tAa/tGa|*454|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:731,0,933
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4786 chr1 183134 . G C 1853.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=19.9966;MLEAC=2;MLEAF=1.00;MQ=59.84;MQ0=0;QD=28.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,47:48:99:1882,141,0
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|
4787 chr1 183164 . G A 1985.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.89;MQ0=0;QD=23.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:2014,153,0
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|
|
4788 chr1 183180 . A T 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=53;Dels=0.00;FS=2.623;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=-0.670;QD=13.92;ReadPosRankSum=0.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:766,0,944
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|
|
4789 chr1 183192 . C T 1829.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=4.4532;MLEAC=2;MLEAF=1.00;MQ=59.89;MQ0=0;QD=33.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:1858,150,0
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|
|
4790 chr1 183206 . C T 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.194;DP=47;Dels=0.00;FS=2.919;HaplotypeScore=3.7882;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=0.613;QD=12.29;ReadPosRankSum=0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:606,0,947
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4791 chr1 183210 . C A 1916.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=2;MLEAF=1.00;MQ=59.92;MQ0=0;QD=30.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1945,147,0
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|
|
4792 chr1 183264 . C G 587.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;DP=38;Dels=0.00;FS=1.237;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-2.646;QD=15.47;ReadPosRankSum=0.073;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:616,0,690
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|
|
4793 chr1 183410 . C A 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.9453;MLEAC=1;MLEAF=0.500;MQ=55.82;MQ0=0;MQRankSum=-1.739;QD=4.72;ReadPosRankSum=-2.268;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:26,7:33:99:184,0,765
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|
4794 chr1 183443 . G A 1009.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.08;MQ0=0;QD=27.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1038,81,0
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|
|
4795 chr1 183460 . C T 838.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.48;MQ0=0;QD=35.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:867,69,0
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|
|
4796 chr1 183464 . G A 858.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.48;MQ0=0;QD=29.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:887,69,0
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|
|
4797 chr1 183493 . C A 473.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.39;MQ0=0;QD=26.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:502,39,0
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|
|
4798 chr1 183509 . A G 339.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.00;MQ0=1;QD=28.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,12:12:30:368,30,0
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|
|
4799 chr1 183531 . G A 267.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.51;MQ0=1;QD=26.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,10:10:24:296,24,0
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|
|
4800 chr1 183542 . T C 237.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=6.6549;MLEAC=2;MLEAF=1.00;MQ=39.61;MQ0=1;QD=23.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,10:10:21:266,21,0
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|
4801 chr1 183564 . G A 265.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.61;MQ0=1;QD=24.16;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:24:294,24,0
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|
4802 chr1 183568 . A G 273.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.61;MQ0=1;QD=24.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:24:302,24,0
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|
|
4803 chr1 183569 . C T 272.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.61;MQ0=1;QD=24.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:24:301,24,0
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|
4804 chr1 183580 . G T 378.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.45;MQ0=1;QD=23.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,16:16:33:407,33,0
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|
4805 chr1 183601 . C T 413.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=2;MLEAF=1.00;MQ=36.53;MQ0=0;QD=27.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,15:15:36:442,36,0
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|
4806 chr1 183602 . G C 414.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=2;MLEAF=1.00;MQ=36.53;MQ0=0;QD=27.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,15:15:36:443,36,0
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|
|
4807 chr1 183606 . C T 458.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.57;MQ0=0;QD=25.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,18:18:39:487,39,0
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|
|
4808 chr1 183618 . C T 490.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.82;MQ0=0;QD=25.83;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,19:19:42:519,42,0
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|
4809 chr1 183623 . A G 484.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.91;MQ0=1;QD=24.24;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,20:20:42:513,42,0
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|
4810 chr1 183645 . A G 560.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=1;QD=26.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,21:21:48:589,48,0
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|
4811 chr1 183881 . T C 84.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.25;MQ0=1;QD=14.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,6:6:12:112,12,0
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|
4812 chr1 184039 . C T 65.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.300;DP=17;Dels=0.00;FS=11.761;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=14.06;MQ0=10;MQRankSum=1.300;QD=3.87;ReadPosRankSum=1.754;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:12,5:17:39:94,0,39
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|
4813 chr1 184048 . G A 68.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.380;DP=14;Dels=0.00;FS=6.990;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.98;MQ0=8;MQRankSum=0.000;QD=4.91;ReadPosRankSum=1.380;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,6:14:25:97,0,25
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4814 chr1 184262 . G A 35.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.39;MQ0=0;QD=17.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:63,6,0
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4815 chr1 184325 . T A 368.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=36.79;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:397,30,0
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|
4816 chr1 184366 . G T 16.86 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.495;DP=7;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.95;MQ0=0;MQRankSum=-1.495;QD=2.41;ReadPosRankSum=1.495;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:5,2:7:45:45,0,172
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|
4817 chr1 184384 . T A 250.8 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.83;MQ0=0;QD=27.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,9:9:21:279,21,0
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|
4818 chr1 184401 . T C 297.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.06;MQ0=0;QD=29.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,10:10:24:326,24,0
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|
4819 chr1 184419 . C T 459.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.09;MQ0=0;QD=32.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,14:14:36:488,36,0
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|
4820 chr1 184437 . A C 589.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.37;MQ0=0;QD=34.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,17:17:45:618,45,0
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|
4821 chr1 184457 . T A 615.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=2;MLEAF=1.00;MQ=57.14;MQ0=0;QD=33.68;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:644,48,0
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|
4822 chr1 184511 . A G 177.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:206,15,0
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|
4823 chr1 184520 . T C 126.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:154,12,0
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|
4824 chr1 184712 . A G 14.68 LowQual AC=2;AF=1.00;AN=2;BaseQRankSum=0.804;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.76;MQ0=5;MQRankSum=0.804;QD=2.10;ReadPosRankSum=0.804;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:6,1:7:3:41,3,0
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|
4825 chr1 184812 . C T 293.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.740;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=2.2460;MLEAC=2;MLEAF=1.00;MQ=38.19;MQ0=1;MQRankSum=1.849;QD=22.60;ReadPosRankSum=-2.589;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:4,9:13:24:322,24,0
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|
4826 chr1 184813 . G A 293.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.382;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=2.2460;MLEAC=2;MLEAF=1.00;MQ=38.19;MQ0=1;MQRankSum=2.262;QD=22.60;ReadPosRankSum=-2.262;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:4,8:13:24:322,24,0
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|
4827 chr1 184816 . T C 293.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.106;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=2.2460;MLEAC=2;MLEAF=1.00;MQ=38.19;MQ0=1;MQRankSum=2.262;QD=22.60;ReadPosRankSum=-0.978;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:3,8:13:24:322,24,0
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|
|
4828 chr1 184870 . C G 77.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.27;MQ0=0;QD=25.76;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:105,9,0
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|
4829 chr1 184877 . A C 110.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.51;MQ0=0;QD=27.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:138,12,0
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|
|
4830 chr1 184924 . T C 381.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.07;MQ0=0;QD=34.71;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:410,33,0
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|
4831 chr1 184928 . A G 414.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.28;MQ0=0;QD=34.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,12:12:36:443,36,0
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|
|
4832 chr1 184947 . T C 553.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.40;MQ0=0;QD=29.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:582,45,0
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|
|
4833 chr1 184967 . G A 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.750;DP=26;Dels=0.00;FS=4.435;HaplotypeScore=2.6549;MLEAC=1;MLEAF=0.500;MQ=52.68;MQ0=0;MQRankSum=-3.139;QD=6.91;ReadPosRankSum=-2.639;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:208,0,643
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|
|
4834 chr1 184971 . G C 238.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.026;DP=27;Dels=0.00;FS=6.965;HaplotypeScore=2.6549;MLEAC=1;MLEAF=0.500;MQ=52.77;MQ0=0;MQRankSum=-3.060;QD=8.84;ReadPosRankSum=-1.672;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,9:27:99:267,0,627
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|
|
4835 chr1 184992 . C A 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.420;DP=30;Dels=0.00;FS=3.779;HaplotypeScore=7.2988;MLEAC=1;MLEAF=0.500;MQ=55.33;MQ0=0;MQRankSum=-3.443;QD=10.59;ReadPosRankSum=0.344;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,11:30:99:346,0,566
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|
|
4836 chr1 184999 . G A 589.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.172;DP=36;Dels=0.00;FS=2.798;HaplotypeScore=2.3001;MLEAC=1;MLEAF=0.500;MQ=57.43;MQ0=0;MQRankSum=-2.789;QD=16.38;ReadPosRankSum=-2.345;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,19:36:99:618,0,532
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|
|
4837 chr1 185038 . A T 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.418;DP=37;Dels=0.00;FS=5.015;HaplotypeScore=1.9983;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-0.820;QD=19.32;ReadPosRankSum=2.088;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:15,22:37:99:743,0,477
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|
|
4838 chr1 185039 . T A 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.072;DP=39;Dels=0.00;FS=4.649;HaplotypeScore=1.9983;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=0.736;QD=11.46;ReadPosRankSum=-1.833;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,15:39:99:475,0,785
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|
|
4839 chr1 185068 . A T 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.341;DP=40;Dels=0.00;FS=6.983;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=1.559;QD=19.29;ReadPosRankSum=0.657;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,23:40:99:800,0,540
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|
|
4840 chr1 185070 . C G 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.143;DP=41;Dels=0.00;FS=9.282;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.801;QD=18.68;ReadPosRankSum=0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,23:41:99:794,0,571
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|
|
4841 chr1 185084 . C A 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.442;DP=41;Dels=0.00;FS=6.934;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.781;QD=18.95;ReadPosRankSum=-0.966;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,24:41:99:805,0,519
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|
|
4842 chr1 185087 . G A 1558.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=59.86;MQ0=0;QD=32.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1587,120,0
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|
|
4843 chr1 185096 . A G 492.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.414;DP=37;Dels=0.00;FS=5.209;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=0.383;QD=13.32;ReadPosRankSum=1.364;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:521,0,697
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|
|
4844 chr1 185113 . T C 1279.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=0;QD=28.25;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1308,99,0
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|
|
4845 chr1 185114 . G A 1207.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=0;QD=33.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1236,93,0
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|
|
4846 chr1 185129 . C A 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.123;DP=36;Dels=0.00;FS=2.788;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=0.459;QD=15.88;ReadPosRankSum=0.111;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,18:36:99:600,0,584
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|
|
4847 chr1 185138 . C G 543.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.656;DP=37;Dels=0.00;FS=1.289;HaplotypeScore=14.8277;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=1.595;QD=14.70;ReadPosRankSum=-0.228;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:572,0,645
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|
|
4848 chr1 185141 . G A 535.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.601;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=14.8277;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-1.139;QD=15.31;ReadPosRankSum=0.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:564,0,590
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|
|
4849 chr1 185145 . G T 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.115;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-1.139;QD=14.36;ReadPosRankSum=0.886;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:502,0,598
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|
|
4850 chr1 185186 . C T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.484;DP=37;Dels=0.00;FS=1.280;HaplotypeScore=19.3302;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.960;QD=16.40;ReadPosRankSum=0.137;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:635,0,578
|
|
|
4851 chr1 185222 . T A 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.397;DP=45;Dels=0.00;FS=1.154;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.101;QD=16.48;ReadPosRankSum=1.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,23:45:99:770,0,755
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|
|
4852 chr1 185241 . A G 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.630;DP=48;Dels=0.00;FS=2.415;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.103;QD=15.31;ReadPosRankSum=0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:763,0,865
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|
|
4853 chr1 185245 . G A 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.011;DP=48;Dels=0.00;FS=2.415;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.619;QD=15.29;ReadPosRankSum=-0.433;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:762,0,868
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|
|
4854 chr1 185259 . C T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.633;DP=49;Dels=0.00;FS=2.460;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-1.136;QD=13.95;ReadPosRankSum=-0.915;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:712,0,900
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|
|
4855 chr1 185264 . T C 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.367;DP=52;Dels=0.00;FS=1.072;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=-1.606;QD=14.51;ReadPosRankSum=-1.404;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:783,0,962
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|
|
4856 chr1 185289 . C T 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.904;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.8940;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=0;MQRankSum=-1.022;QD=12.65;ReadPosRankSum=-0.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:623,0,933
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|
|
4857 chr1 185299 . A T 506.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.800;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=16.4921;MLEAC=1;MLEAF=0.500;MQ=58.05;MQ0=0;MQRankSum=-2.184;QD=11.52;ReadPosRankSum=0.752;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:535,0,917
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|
|
4858 chr1 185346 . C T 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.206;DP=33;Dels=0.00;FS=8.695;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=-3.050;QD=9.45;ReadPosRankSum=1.815;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:340,0,747
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|
|
4859 chr1 185347 . A G 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.318;DP=33;Dels=0.00;FS=11.504;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=-2.826;QD=10.57;ReadPosRankSum=1.890;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:377,0,759
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|
|
4860 chr1 185372 . T C 246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.574;DP=29;Dels=0.00;FS=17.193;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.21;MQ0=0;MQRankSum=-4.382;QD=8.51;ReadPosRankSum=0.482;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:275,0,692
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|
|
4861 chr1 185376 . C G 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.478;DP=28;Dels=0.00;FS=21.622;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-3.926;QD=5.49;ReadPosRankSum=1.804;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:182,0,778
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|
|
4862 chr1 185383 . C T 118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.318;DP=28;Dels=0.00;FS=16.983;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-3.926;QD=4.24;ReadPosRankSum=0.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:147,0,783
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|
|
4863 chr1 185387 . A G 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.478;DP=28;Dels=0.00;FS=19.859;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-3.926;QD=4.81;ReadPosRankSum=0.212;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:163,0,736
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|
|
4864 chr1 185394 . A C 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.146;DP=27;Dels=0.00;FS=16.983;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.70;MQ0=0;MQRankSum=-3.703;QD=4.25;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,6:27:99:143,0,783
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|
|
4865 chr1 185401 . T A 111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.242;DP=29;Dels=0.00;FS=15.529;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.86;MQ0=0;MQRankSum=-3.742;QD=3.85;ReadPosRankSum=-0.673;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,6:29:99:140,0,846
|
|
|
4866 chr1 185407 . C T 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.867;DP=23;Dels=0.00;FS=6.628;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=-2.784;QD=0.86;ReadPosRankSum=-2.784;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,3:23:48:48,0,737
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|
|
4867 chr1 185480 . G A 732.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=62.24;MQ0=0;QD=30.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:761,57,0
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|
|
4868 chr1 185486 . C T 684.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=62.24;MQ0=0;QD=29.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,19:19:54:713,54,0
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|
|
4869 chr1 185509 . T C 606.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=62.65;MQ0=0;QD=28.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:635,48,0
|
|
|
4870 chr1 185547 . C T 637.94 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.964;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.91;MQ0=0;MQRankSum=-1.156;QD=24.50;ReadPosRankSum=1.349;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:1,17:18:14:666,14,0
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|
|
4871 chr1 185642 . A T 574.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.69;MQ0=0;QD=28.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:603,45,0
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|
|
4872 chr1 185689 . A C 173.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.167;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.58;MQ0=1;MQRankSum=-2.906;QD=7.24;ReadPosRankSum=-1.837;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:16,8:24:99:202,0,578
|
|
|
4873 chr1 185691 . T G 889.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.58;MQ0=1;QD=27.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,24:24:69:918,69,0
|
|
|
4874 chr1 185717 . A G 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.307;DP=33;Dels=0.00;FS=3.365;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.82;MQ0=1;MQRankSum=-1.880;QD=10.51;ReadPosRankSum=0.998;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:375,0,665
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|
|
4875 chr1 185726 . G C 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.175;DP=39;Dels=0.00;FS=4.887;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=1;MQRankSum=-2.190;QD=15.22;ReadPosRankSum=0.234;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:622,0,634
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|
|
4876 chr1 185747 . A T 894.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.281;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.36;MQ0=1;MQRankSum=-1.881;QD=20.81;ReadPosRankSum=-0.894;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:14,29:43:99:923,0,453
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|
|
4877 chr1 185776 . A G 872.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.350;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.87;MQ0=1;MQRankSum=-1.287;QD=22.38;ReadPosRankSum=2.961;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:11,28:39:99:901,0,314
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|
|
4878 chr1 185800 . C T 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.468;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=4.9825;MLEAC=1;MLEAF=0.500;MQ=50.92;MQ0=1;MQRankSum=-0.406;QD=25.35;ReadPosRankSum=1.529;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:5,23:28:89:738,0,89
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|
|
4879 chr1 185804 . T G 590.81 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.175;DP=28;Dels=0.00;FS=8.073;HaplotypeScore=5.6476;MLEAC=1;MLEAF=0.500;MQ=49.66;MQ0=1;MQRankSum=1.135;QD=21.10;ReadPosRankSum=0.436;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:3,22:28:16:690,0,16
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|
|
4880 chr1 185818 . T G 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.771;DP=24;Dels=0.00;FS=2.570;HaplotypeScore=2.9824;MLEAC=1;MLEAF=0.500;MQ=47.71;MQ0=1;MQRankSum=1.176;QD=24.03;ReadPosRankSum=-0.852;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:4,20:24:53:605,0,53
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|
|
4881 chr1 186025 . A C 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=1.9066;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;QD=4.46;ReadPosRankSum=1.026;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:2,2:4:46:46,0,47
|
|
|
4882 chr1 186043 . A G 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.207;DP=38;Dels=0.00;FS=3.067;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.26;MQ0=5;MQRankSum=-1.963;QD=15.02;ReadPosRankSum=-2.900;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:599,0,549
|
|
|
4883 chr1 186058 . T A 1383.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.62;MQ0=5;QD=34.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1412,105,0
|
|
|
4884 chr1 186081 . A G 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.401;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=0;MQRankSum=-0.474;QD=15.86;ReadPosRankSum=2.879;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:710,0,742
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|
|
4885 chr1 186083 . T A 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.085;DP=43;Dels=0.00;FS=1.177;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=2.928;QD=16.48;ReadPosRankSum=-2.126;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:737,0,714
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|
|
4886 chr1 186128 . C G 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.528;DP=39;Dels=0.00;FS=1.390;HaplotypeScore=19.8272;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.043;QD=12.22;ReadPosRankSum=-0.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,16:39:99:505,0,805
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|
|
4887 chr1 186204 . A T 1634.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=2;MLEAF=1.00;MQ=52.86;MQ0=7;QD=30.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:1663,126,0
|
|
|
4888 chr1 186205 . G C 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.966;DP=52;Dels=0.00;FS=2.716;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=52.72;MQ0=7;MQRankSum=0.198;QD=8.55;ReadPosRankSum=-0.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,19:52:99:473,0,903
|
|
|
4889 chr1 186248 . C T 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.117;DP=39;Dels=0.00;FS=2.991;HaplotypeScore=12.5646;MLEAC=1;MLEAF=0.500;MQ=51.44;MQ0=4;MQRankSum=-0.750;QD=13.92;ReadPosRankSum=0.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:571,0,491
|
|
|
4890 chr1 186252 . T C 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=38;Dels=0.00;FS=1.412;HaplotypeScore=14.4976;MLEAC=1;MLEAF=0.500;MQ=52.11;MQ0=3;MQRankSum=-1.250;QD=14.41;ReadPosRankSum=0.383;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,20:38:99:576,0,472
|
|
|
4891 chr1 186263 . T C 466.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.915;DP=45;Dels=0.00;FS=1.264;HaplotypeScore=23.4286;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=2.794;QD=10.37;ReadPosRankSum=-0.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:28,17:45:99:495,0,824
|
|
|
4892 chr1 186273 . C T 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.092;DP=50;Dels=0.00;FS=8.671;HaplotypeScore=22.6968;MLEAC=1;MLEAF=0.500;MQ=55.43;MQ0=1;MQRankSum=3.184;QD=12.62;ReadPosRankSum=1.495;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:659,0,894
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|
|
4893 chr1 186302 . T C 961.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.434;DP=49;Dels=0.00;FS=5.993;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=-0.254;QD=19.63;ReadPosRankSum=0.315;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,29:49:99:990,0,585
|
|
|
4894 chr1 186305 . G A 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.336;DP=45;Dels=0.00;FS=2.751;HaplotypeScore=2.8649;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-1.332;QD=18.73;ReadPosRankSum=-0.081;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,27:45:99:871,0,521
|
|
|
4895 chr1 186318 . T C 531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.825;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.9982;MLEAC=1;MLEAF=0.500;MQ=56.94;MQ0=0;MQRankSum=2.087;QD=10.03;ReadPosRankSum=-0.213;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:34,19:53:99:560,0,1118
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|
4896 chr1 186366 . G A 683.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.40;MQ0=0;QD=32.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:712,54,0
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|
|
4897 chr1 186382 . G A 56.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.17;MQ0=0;QD=28.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0
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|
|
4898 chr1 186396 . T C 397.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.194;DP=18;Dels=0.00;FS=2.762;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=35.37;MQ0=0;MQRankSum=-1.756;QD=22.10;ReadPosRankSum=-2.318;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:2,16:18:34:426,0,34
|
|
|
4899 chr1 186407 . T C 557.81 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.691;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=35.89;MQ0=0;MQRankSum=-1.909;QD=24.25;ReadPosRankSum=-2.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:2,21:23:20:586,0,20
|
|
|
4900 chr1 186440 . C A 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.795;DP=31;Dels=0.00;FS=19.193;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.71;MQ0=0;MQRankSum=3.153;QD=1.48;ReadPosRankSum=-2.740;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,4:31:74:74,0,835
|
|
|
4901 chr1 186449 . C A 1104.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=44.29;MQ0=0;QD=28.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1133,90,0
|
|
|
4902 chr1 186454 . C T 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.649;DP=34;Dels=0.00;FS=22.252;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.56;MQ0=0;MQRankSum=-3.817;QD=27.05;ReadPosRankSum=2.372;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:6,28:34:99:948,0,144
|
|
|
4903 chr1 186460 . C T 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.748;DP=32;Dels=0.00;FS=17.527;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=46.19;MQ0=0;MQRankSum=-3.790;QD=26.90;ReadPosRankSum=2.245;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:6,26:32:99:889,0,146
|
|
|
4904 chr1 186464 . T C 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.469;DP=34;Dels=0.00;FS=19.762;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=46.63;MQ0=0;MQRankSum=-4.046;QD=25.85;ReadPosRankSum=1.704;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:7,27:34:99:907,0,182
|
|
|
4905 chr1 186478 . T C 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=25;Dels=0.00;FS=15.830;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=49.25;MQ0=0;MQRankSum=-3.990;QD=21.03;ReadPosRankSum=-0.379;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,17:25:99:554,0,243
|
|
|
4906 chr1 186480 . A C 212.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=25;Dels=0.00;FS=15.830;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=49.25;MQ0=0;MQRankSum=3.932;QD=8.51;ReadPosRankSum=1.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:241,0,553
|
|
|
4907 chr1 186483 . C T 883.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.9916;MLEAC=2;MLEAF=1.00;MQ=50.06;MQ0=0;QD=31.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,24:24:72:912,72,0
|
|
|
4908 chr1 186485 . A G 470.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.452;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.47;ReadPosRankSum=-1.517;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:499,0,249
|
|
|
4909 chr1 186488 . C T 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.290;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=19.60;ReadPosRankSum=-1.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:479,0,255
|
|
|
4910 chr1 186496 . G T 463.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.613;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.16;ReadPosRankSum=-1.130;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:492,0,235
|
|
|
4911 chr1 186499 . T C 462.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.065;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.12;ReadPosRankSum=-0.484;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:491,0,247
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|
|
4912 chr1 186500 . T C 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.807;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.08;ReadPosRankSum=-0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:490,0,245
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|
4913 chr1 186522 . A G 162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.798;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.47;MQ0=0;MQRankSum=3.201;QD=8.57;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:13,6:19:99:191,0,365
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|
4914 chr1 186527 . T A 262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.452;DP=18;Dels=0.00;FS=2.762;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.08;MQ0=0;MQRankSum=-3.138;QD=14.60;ReadPosRankSum=0.140;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:6,12:18:99:291,0,198
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|
4915 chr1 186553 . C T 134.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.05;MQ0=0;QD=33.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:162,12,0
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|
4916 chr1 186562 . C T 97.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.600;DP=12;Dels=0.00;FS=6.818;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.72;MQ0=0;MQRankSum=2.637;QD=8.15;ReadPosRankSum=0.825;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,4:12:99:126,0,256
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|
4917 chr1 186565 . C T 383.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.26;MQ0=0;QD=34.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:412,33,0
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|
4918 chr1 186581 . C T 24.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.296;DP=11;Dels=0.00;FS=3.310;HaplotypeScore=1.7987;MLEAC=1;MLEAF=0.500;MQ=42.26;MQ0=0;MQRankSum=2.003;QD=2.25;ReadPosRankSum=2.003;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:9,2:11:53:53,0,266
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|
4919 chr1 186587 . A G 52.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.02;MQ0=0;MQRankSum=0.736;QD=17.58;ReadPosRankSum=0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:1,2:3:6:80,6,0
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|
4920 chr1 186588 . T C 53.74 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.02;MQ0=0;QD=17.91;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,3:3:6:81,6,0
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|
4921 chr1 186590 . T C 44.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.02;MQ0=0;MQRankSum=0.736;QD=14.93;ReadPosRankSum=0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:1,2:3:26:73,0,26
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4922 chr1 186605 . C T 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;DP=28;Dels=0.00;FS=12.091;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.49;MQ0=0;MQRankSum=3.575;QD=20.53;ReadPosRankSum=-3.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:11,17:28:99:603,0,347
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|
4923 chr1 186611 . A G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.292;DP=29;Dels=0.00;FS=8.572;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=0;MQRankSum=-3.843;QD=11.44;ReadPosRankSum=2.854;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,11:29:99:360,0,648
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4924 chr1 186614 . C T 339.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.067;DP=29;Dels=0.00;FS=8.572;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=0;MQRankSum=-3.798;QD=11.72;ReadPosRankSum=2.944;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,11:29:99:368,0,655
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|
4925 chr1 186624 . C T 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.559;DP=34;Dels=0.00;FS=11.031;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=57.15;MQ0=0;MQRankSum=-4.146;QD=11.32;ReadPosRankSum=2.055;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,13:34:99:413,0,758
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|
4926 chr1 186629 . C T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.439;DP=38;Dels=0.00;FS=8.924;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=0;MQRankSum=4.390;QD=20.20;ReadPosRankSum=-0.695;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:16,22:38:99:796,0,505
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|
4927 chr1 186638 . G A 1706.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.64;MQ0=0;QD=24.81;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1735,129,0
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|
4928 chr1 186658 . C T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;DP=53;Dels=0.00;FS=6.435;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=-3.592;QD=11.94;ReadPosRankSum=-1.373;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,21:53:99:661,0,1102
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4929 chr1 186661 . C T 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.611;DP=54;Dels=0.00;FS=6.487;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQ0=0;MQRankSum=-3.283;QD=12.29;ReadPosRankSum=-1.276;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:692,0,1121
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4930 chr1 186663 . C T 1074.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.185;DP=57;Dels=0.00;FS=8.033;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=3.964;QD=18.86;ReadPosRankSum=1.552;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,32:57:99:1103,0,821
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4931 chr1 186666 . G A 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.687;DP=56;Dels=0.00;FS=6.180;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=3.767;QD=19.30;ReadPosRankSum=0.538;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1109,0,798
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4932 chr1 186683 . A C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.388;DP=53;Dels=0.00;FS=1.158;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-3.312;QD=12.86;ReadPosRankSum=1.200;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:710,0,1078
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4933 chr1 186694 . T C 1666.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=30.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1695,126,0
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4934 chr1 186695 . C T 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.467;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=4.002;QD=16.74;ReadPosRankSum=0.786;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:765,0,705
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4935 chr1 186696 . C T 738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.300;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=3.924;QD=17.18;ReadPosRankSum=0.668;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:767,0,660
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4936 chr1 186702 . C T 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.286;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.080;QD=13.35;ReadPosRankSum=0.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:629,0,825
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4937 chr1 186707 . G A 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.442;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.738;QD=15.75;ReadPosRankSum=0.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:737,0,782
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4938 chr1 186723 . G A 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.815;DP=40;Dels=0.00;FS=2.843;HaplotypeScore=5.9981;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=-0.650;QD=16.19;ReadPosRankSum=-1.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,21:40:99:676,0,656
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4939 chr1 186725 . G A 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.320;DP=41;Dels=0.00;FS=4.533;HaplotypeScore=5.9981;MLEAC=1;MLEAF=0.500;MQ=59.70;MQ0=0;MQRankSum=-0.588;QD=16.65;ReadPosRankSum=-1.216;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:711,0,635
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4940 chr1 186730 . C T 120.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.280;DP=43;Dels=0.00;FS=6.398;HaplotypeScore=7.8644;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.477;QD=2.81;ReadPosRankSum=0.609;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:36,7:43:99:149,0,1300
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|
4941 chr1 186735 . T C 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.621;DP=43;Dels=0.00;FS=4.425;HaplotypeScore=7.8644;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-1.278;QD=14.62;ReadPosRankSum=-0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:657,0,661
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|
4942 chr1 186738 . C T 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.029;DP=43;Dels=0.00;FS=1.242;HaplotypeScore=7.8644;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.109;QD=14.95;ReadPosRankSum=-0.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:671,0,692
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|
|
4943 chr1 186794 . C A 2054.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=32.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2083,157,0
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|
|
4944 chr1 186799 . A C 2004.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.39;MQ0=0;QD=29.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:2033,154,0
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|
|
4945 chr1 186800 . T C 892.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.425;DP=51;Dels=0.00;FS=3.975;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.519;QD=17.51;ReadPosRankSum=0.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:921,0,810
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|
|
4946 chr1 186804 . C T 2108.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.45;MQ0=0;QD=28.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2137,166,0
|
|
|
4947 chr1 186814 . G A 2540.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=1.7339;MLEAC=2;MLEAF=1.00;MQ=59.52;MQ0=0;QD=29.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,65:65:99:2569,196,0
|
|
|
4948 chr1 186823 . T C 2655.77 . AC=2;AF=1.00;AN=2;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=1.7339;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=0;QD=27.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,67:67:99:2684,202,0
|
|
|
4949 chr1 186853 . A G 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.007;DP=60;Dels=0.00;FS=1.028;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.037;QD=13.25;ReadPosRankSum=-1.052;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:823,0,1142
|
|
|
4950 chr1 186856 . A G 1066.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.908;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.735;QD=17.49;ReadPosRankSum=1.096;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,34:61:99:1095,0,816
|
|
|
4951 chr1 186871 . C T 2064.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.64;MQ0=0;QD=34.20;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2093,160,0
|
|
|
4952 chr1 186897 . A G 1641.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1670,129,0
|
|
|
4953 chr1 186922 . C T 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.042;DP=39;Dels=0.00;FS=10.184;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.363;QD=15.74;ReadPosRankSum=0.576;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:642,0,675
|
|
|
4954 chr1 186958 . T G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.769;DP=38;Dels=0.00;FS=9.513;HaplotypeScore=2.7878;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=-0.015;QD=15.89;ReadPosRankSum=-0.482;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:632,0,693
|
|
|
4955 chr1 186977 . T C 1690.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.26;MQ0=0;QD=33.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1719,129,0
|
|
|
4956 chr1 186990 . T A 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.733;DP=43;Dels=0.00;FS=1.194;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=1.494;QD=16.67;ReadPosRankSum=-0.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:745,0,730
|
|
|
4957 chr1 186991 . G A 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.624;DP=42;Dels=0.00;FS=1.170;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=-2.632;QD=15.64;ReadPosRankSum=0.743;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:685,0,742
|
|
|
4958 chr1 186992 . C T 627.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.654;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=0;MQRankSum=-1.503;QD=15.31;ReadPosRankSum=0.980;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:656,0,735
|
|
|
4959 chr1 187055 . G A 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.270;DP=49;Dels=0.00;FS=6.133;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=-1.990;QD=15.77;ReadPosRankSum=-0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:801,0,876
|
|
|
4960 chr1 187064 . A G 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.160;DP=47;Dels=0.00;FS=6.439;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=-1.075;QD=16.42;ReadPosRankSum=-0.990;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:800,0,846
|
|
|
4961 chr1 187065 . G A 768.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=46;Dels=0.00;FS=6.548;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;MQRankSum=-0.923;QD=16.71;ReadPosRankSum=-1.186;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:797,0,815
|
|
|
4962 chr1 187147 . C T 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.158;DP=43;Dels=0.00;FS=1.192;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.400;QD=15.06;ReadPosRankSum=-0.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:676,0,759
|
|
|
4963 chr1 187173 . A T 804.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.160;DP=51;Dels=0.00;FS=1.128;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.970;QD=15.78;ReadPosRankSum=-0.688;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:833,0,844
|
|
|
4964 chr1 187185 . A T 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.328;DP=59;Dels=0.00;FS=1.046;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.148;QD=15.59;ReadPosRankSum=1.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:31,28:59:99:948,0,1051
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|
|
4965 chr1 187200 . T C 218.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.286;DP=70;Dels=0.00;FS=12.081;HaplotypeScore=23.9717;MLEAC=1;MLEAF=0.500;MQ=56.69;MQ0=0;MQRankSum=-5.431;QD=3.13;ReadPosRankSum=-3.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:58,12:70:99:247,0,2146
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|
|
4966 chr1 187208 . T G 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.365;DP=73;Dels=0.00;FS=9.609;HaplotypeScore=23.9717;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=0;MQRankSum=-5.455;QD=2.83;ReadPosRankSum=-2.746;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:61,12:73:99:235,0,2122
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|
|
4967 chr1 187209 . A C 990.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.151;DP=73;Dels=0.00;FS=1.959;HaplotypeScore=23.9717;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=0;MQRankSum=2.896;QD=13.57;ReadPosRankSum=1.981;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:42,31:73:99:1019,0,1427
|
|
|
4968 chr1 187247 . G A 1055.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.510;DP=55;Dels=0.00;FS=2.329;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.33;MQ0=0;MQRankSum=-1.357;QD=19.20;ReadPosRankSum=-1.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1084,0,781
|
|
|
4969 chr1 187248 . G T 963.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.193;DP=53;Dels=0.00;FS=3.850;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=0;MQRankSum=-1.911;QD=18.18;ReadPosRankSum=-0.763;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,30:53:99:992,0,786
|
|
|
4970 chr1 187270 . C G 518.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.820;DP=38;Dels=0.00;FS=2.937;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.61;MQ0=0;MQRankSum=-5.255;QD=13.65;ReadPosRankSum=3.582;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:547,0,742
|
|
|
4971 chr1 187298 . C T 1101.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.354;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.65;MQ0=0;MQRankSum=0.258;QD=21.60;ReadPosRankSum=1.685;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:15,36:51:99:1130,0,459
|
|
|
4972 chr1 187302 . A G 1787.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.82;MQ0=0;QD=32.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1816,135,0
|
|
|
4973 chr1 187346 . C T 972.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.918;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.31;MQ0=3;MQRankSum=2.275;QD=31.38;ReadPosRankSum=1.918;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:5,26:31:78:1001,78,0
|
|
|
4974 chr1 187362 . T C 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.168;DP=38;Dels=0.00;FS=1.434;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.20;MQ0=4;MQRankSum=-2.189;QD=9.18;ReadPosRankSum=0.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,13:38:99:377,0,655
|
|
|
4975 chr1 187385 . C T 1261.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=2;MLEAF=1.00;MQ=54.34;MQ0=3;QD=34.10;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:2,35:37:99:1290,99,0
|
|
|
4976 chr1 187414 . C A 1254.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.94;MQ0=0;QD=26.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1283,99,0
|
|
|
4977 chr1 187461 . C A 765.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.91;MQ0=0;QD=29.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:794,60,0
|
|
|
4978 chr1 187503 . G A 696.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.86;MQ0=0;QD=34.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,19:19:54:725,54,0
|
|
|
4979 chr1 187522 . A T 1152.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.33;MQ0=0;QD=31.26;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1181,90,0
|
|
|
4980 chr1 187574 . T A 1364.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.88;MQ0=2;QD=28.79;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:2,36:38:99:1393,108,0
|
|
|
4981 chr1 187614 . A G 872.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.29;MQ0=2;QD=33.57;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,25:26:69:901,69,0
|
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4982 chr1 187714 . G C 1203.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.78;MQ0=2;QD=28.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,42:42:96:1232,96,0
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4983 chr1 187753 . T C 851.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.068;DP=59;Dels=0.00;FS=1.104;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.49;MQ0=0;MQRankSum=0.555;QD=14.44;ReadPosRankSum=-5.759;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:880,0,1099
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4984 chr1 187793 . T C 1189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.870;DP=60;Dels=0.00;FS=1.043;HaplotypeScore=15.7240;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.945;QD=19.83;ReadPosRankSum=3.344;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1218,0,816
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4985 chr1 187844 . T C 876.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.394;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.259;QD=21.38;ReadPosRankSum=-0.014;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:15,26:41:99:905,0,488
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4986 chr1 187894 . G A 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.395;DP=46;Dels=0.00;FS=4.031;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.055;QD=15.97;ReadPosRankSum=-0.483;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:763,0,746
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4987 chr1 187903 . C T 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;DP=46;Dels=0.00;FS=6.439;HaplotypeScore=4.0994;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=0.791;QD=16.86;ReadPosRankSum=-0.769;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:804,0,717
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4988 chr1 188013 . T A 834.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.499;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=1.291;QD=16.37;ReadPosRankSum=0.725;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:863,0,808
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4989 chr1 188103 . G A 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.073;DP=55;Dels=0.00;FS=4.032;HaplotypeScore=2.6641;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=0.347;QD=14.07;ReadPosRankSum=0.566;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:30,25:55:99:802,0,993
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4990 chr1 188173 . G A 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.617;DP=42;Dels=0.00;FS=2.786;HaplotypeScore=1.9991;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.013;QD=16.61;ReadPosRankSum=1.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:20,22:42:99:726,0,669
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4991 chr1 188266 . A G 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.261;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=3.8663;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.827;QD=15.69;ReadPosRankSum=0.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:28,27:56:99:907,0,965
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4992 chr1 188270 . A G 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.747;DP=54;Dels=0.00;FS=3.828;HaplotypeScore=4.8662;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.692;QD=15.75;ReadPosRankSum=0.709;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:27,27:54:99:879,0,898
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4993 chr1 188311 . T G 901.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=53;Dels=0.00;FS=2.345;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.454;QD=17.01;ReadPosRankSum=0.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:25,28:53:99:930,0,831
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4994 chr1 188357 . C T 1327.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1356,105,0
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4995 chr1 188364 . G C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.285;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.585;QD=14.47;ReadPosRankSum=-0.612;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:22,18:40:99:607,0,770
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4996 chr1 188393 . T C 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.106;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=2.5781;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.191;QD=12.28;ReadPosRankSum=-1.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:24,18:42:99:544,0,828
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4997 chr1 188395 . C G 543.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.484;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=2.5781;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.775;QD=13.26;ReadPosRankSum=-1.773;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:23,18:41:99:572,0,791
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4998 chr1 188416 . T C 397.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=39;Dels=0.00;FS=1.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.893;QD=10.20;ReadPosRankSum=0.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:25,14:39:99:426,0,821
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4999 chr1 188438 . C A 930.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.123;DP=50;Dels=0.00;FS=5.900;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=0.020;QD=18.62;ReadPosRankSum=-0.472;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:21,29:50:99:959,0,659
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5000 chr1 188621 . G A 704.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=49;Dels=0.00;FS=5.986;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.090;QD=14.38;ReadPosRankSum=-0.774;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L4|Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:27,22:49:99:733,0,926
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