annotate test-data/01_1787_FL_Zoo_Jaguar.vcf @ 13:cd636b0e4f95 draft

"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit cab8ee43e902a3ae7b0fd6b06842c4b5c221af25"
author greg
date Tue, 21 Sep 2021 00:21:36 +0000
parents da20c7c76d06
children
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1 ##fileformat=VCFv4.2
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2 ##FILTER=<ID=LowQual,Description="Low quality">
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3 ##FORMAT=<ID=AD,Number=R,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.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.8-0-ge9d806836,Date="Fri Dec 22 16:41:19 CST 2017",Epoch=1513982479531,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/scratch/analysis_staging/a_script/bovis_reanalysis_af2122_2017-12-14/2001-2008/01-1787/01-1787-quality.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/scratch/analysis_staging/a_script/bovis_reanalysis_af2122_2017-12-14/2001-2008/01-1787/NC_002945v4.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 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 variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false out=/scratch/analysis_staging/a_script/bovis_reanalysis_af2122_2017-12-14/2001-2008/01-1787/01-1787-hapall.vcf likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[] excludeAnnotation=[] group=[StandardAnnotation, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=true numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=true keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=true captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 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=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
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14 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
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15 ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
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16 ##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
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17 ##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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18 ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
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19 ##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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20 ##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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21 ##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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22 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
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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=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
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26 ##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
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27 ##contig=<ID=NC_002945.4,length=4349904>
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28 ##reference=file:///scratch/analysis_staging/a_script/bovis_reanalysis_af2122_2017-12-14/2001-2008/01-1787/NC_002945v4.fasta
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29 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 01-1787
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30 NC_002945.4 1057 . A G 10912.77 . AC=2;AF=1.00;AN=2;DP=397;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.56;SOR=0.703 GT:AD:DP:GQ:PL 1/1:0,396:396:99:10941,1177,0
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31 NC_002945.4 8741 . T C 8362.77 . AC=2;AF=1.00;AN=2;DP=250;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.45;SOR=1.392 GT:AD:DP:GQ:PL 1/1:0,250:250:99:8391,748,0
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32 NC_002945.4 14487 . C G 6175.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.669;ClippingRankSum=0.000;DP=165;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=31.88;ReadPosRankSum=-0.324;SOR=4.804 GT:AD:DP:GQ:PL 1/1:1,159:160:99:6204,468,0
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33 NC_002945.4 33788 . A G 7640.77 . AC=2;AF=1.00;AN=2;DP=180;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.31;SOR=4.828 GT:AD:DP:GQ:PL 1/1:0,180:180:99:7669,542,0
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34 NC_002945.4 41437 . T C 10083.77 . AC=2;AF=1.00;AN=2;DP=342;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.48;SOR=0.870 GT:AD:DP:GQ:PL 1/1:0,342:342:99:10112,1020,0
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35 NC_002945.4 57197 . G C 3714.77 . AC=2;AF=1.00;AN=2;DP=120;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.21;SOR=3.809 GT:AD:DP:GQ:PL 1/1:0,105:105:99:3743,315,0
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36 NC_002945.4 67098 . G A 7793.77 . AC=2;AF=1.00;AN=2;DP=260;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.09;SOR=0.867 GT:AD:DP:GQ:PL 1/1:0,259:259:99:7822,775,0
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37 NC_002945.4 69913 . T C 10036.77 . AC=2;AF=1.00;AN=2;DP=321;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.27;SOR=0.725 GT:AD:DP:GQ:PL 1/1:0,321:321:99:10065,956,0
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38 NC_002945.4 103928 . G C 4649.77 . AC=2;AF=1.00;AN=2;DP=114;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.64;QD=27.17;SOR=2.573 GT:AD:DP:GQ:PL 1/1:0,110:110:99:4678,331,0
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39 NC_002945.4 103931 . G C 4505.77 . AC=2;AF=1.00;AN=2;DP=111;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.18;QD=26.01;SOR=2.509 GT:AD:DP:GQ:PL 1/1:0,107:107:99:4534,321,0
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40 NC_002945.4 104264 . A G 241.80 . AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.54;QD=34.54;SOR=4.174 GT:AD:DP:GQ:PL 1/1:0,7:7:21:270,21,0
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41 NC_002945.4 119328 . G T 12064.77 . AC=2;AF=1.00;AN=2;DP=423;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.52;SOR=0.736 GT:AD:DP:GQ:PL 1/1:0,423:423:99:12093,1260,0
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42 NC_002945.4 127447 . G C 6051.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.843;ClippingRankSum=0.000;DP=196;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=31.52;ReadPosRankSum=-0.504;SOR=0.572 GT:AD:DP:GQ:PL 1/1:1,191:192:99:6080,562,0
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43 NC_002945.4 130237 . T C 8833.77 . AC=2;AF=1.00;AN=2;DP=293;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.15;SOR=1.012 GT:AD:DP:GQ:PL 1/1:0,293:293:99:8862,869,0
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44 NC_002945.4 159370 . A G 6799.77 . AC=2;AF=1.00;AN=2;DP=217;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.34;SOR=0.779 GT:AD:DP:GQ:PL 1/1:0,217:217:99:6828,648,0
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45 NC_002945.4 160535 . T C 8515.77 . AC=2;AF=1.00;AN=2;DP=279;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.63;SOR=1.329 GT:AD:DP:GQ:PL 1/1:0,278:278:99:8544,826,0
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46 NC_002945.4 165799 . G A 8624.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.926;ClippingRankSum=0.000;DP=307;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=28.19;ReadPosRankSum=1.442;SOR=0.272 GT:AD:DP:GQ:PL 1/1:1,305:306:99:8653,897,0
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47 NC_002945.4 166696 . A G 6491.77 . AC=2;AF=1.00;AN=2;DP=214;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.77;SOR=1.079 GT:AD:DP:GQ:PL 1/1:0,211:211:99:6520,627,0
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48 NC_002945.4 180444 . T C 8771.77 . AC=2;AF=1.00;AN=2;DP=315;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.94;SOR=1.168 GT:AD:DP:GQ:PL 1/1:0,314:314:99:8800,931,0
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49 NC_002945.4 182704 . G A 7366.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.976;ClippingRankSum=0.000;DP=272;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=27.49;ReadPosRankSum=1.545;SOR=0.382 GT:AD:DP:GQ:PL 1/1:3,265:268:99:7395,761,0
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50 NC_002945.4 185429 . T C 6597.77 . AC=2;AF=1.00;AN=2;DP=187;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.02;SOR=2.760 GT:AD:DP:GQ:PL 1/1:0,187:187:99:6626,561,0
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51 NC_002945.4 228660 . C T 6295.77 . AC=2;AF=1.00;AN=2;DP=232;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.49;SOR=0.892 GT:AD:DP:GQ:PL 1/1:0,229:229:99:6324,681,0
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52 NC_002945.4 232188 . G C 4879.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.654;ClippingRankSum=0.000;DP=179;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=29.94;ReadPosRankSum=1.419;SOR=0.712 GT:AD:DP:GQ:PL 1/1:1,162:163:99:4908,474,0
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53 NC_002945.4 246207 . C T 8706.77 . AC=2;AF=1.00;AN=2;DP=298;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.22;SOR=0.806 GT:AD:DP:GQ:PL 1/1:0,298:298:99:8735,889,0
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54 NC_002945.4 255465 . A G 9237.77 . AC=2;AF=1.00;AN=2;DP=284;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.53;SOR=0.875 GT:AD:DP:GQ:PL 1/1:0,284:284:99:9266,848,0
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55 NC_002945.4 295519 . T C 9658.77 . AC=2;AF=1.00;AN=2;DP=309;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.36;SOR=0.719 GT:AD:DP:GQ:PL 1/1:0,308:308:99:9687,920,0
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56 NC_002945.4 306689 . N . . . . GT ./.
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57 NC_002945.4 306690 . N . . . . GT ./.
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58 NC_002945.4 306691 . N . . . . GT ./.
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59 NC_002945.4 306692 . N . . . . GT ./.
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60 NC_002945.4 306693 . N . . . . GT ./.
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61 NC_002945.4 306694 . N . . . . GT ./.
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62 NC_002945.4 306695 . N . . . . GT ./.
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63 NC_002945.4 306696 . N . . . . GT ./.
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64 NC_002945.4 306697 . N . . . . GT ./.
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65 NC_002945.4 306698 . N . . . . GT ./.
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66 NC_002945.4 306699 . N . . . . GT ./.
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67 NC_002945.4 306700 . N . . . . GT ./.
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68 NC_002945.4 306701 . N . . . . GT ./.
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69 NC_002945.4 306702 . N . . . . GT ./.
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70 NC_002945.4 306703 . N . . . . GT ./.
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71 NC_002945.4 306704 . N . . . . GT ./.
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72 NC_002945.4 306705 . N . . . . GT ./.
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73 NC_002945.4 306706 . N . . . . GT ./.
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da20c7c76d06 Uploaded
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parents:
diff changeset
1961 NC_002945.4 1634909 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1962 NC_002945.4 1634910 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1963 NC_002945.4 1634911 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1964 NC_002945.4 1634912 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1965 NC_002945.4 1634913 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1966 NC_002945.4 1634914 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1967 NC_002945.4 1634915 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1968 NC_002945.4 1634916 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1969 NC_002945.4 1634917 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1970 NC_002945.4 1634918 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1971 NC_002945.4 1634919 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1972 NC_002945.4 1634920 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1973 NC_002945.4 1634921 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1974 NC_002945.4 1634922 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1975 NC_002945.4 1634923 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1976 NC_002945.4 1634924 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1977 NC_002945.4 1634925 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1978 NC_002945.4 1634926 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1979 NC_002945.4 1634927 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1980 NC_002945.4 1634928 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1981 NC_002945.4 1634929 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1982 NC_002945.4 1634930 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1983 NC_002945.4 1634965 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1984 NC_002945.4 1634966 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1985 NC_002945.4 1634967 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1986 NC_002945.4 1634968 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1987 NC_002945.4 1634969 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1988 NC_002945.4 1634970 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1989 NC_002945.4 1634971 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1990 NC_002945.4 1634972 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1991 NC_002945.4 1634973 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1992 NC_002945.4 1634974 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1993 NC_002945.4 1634975 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1994 NC_002945.4 1634976 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1995 NC_002945.4 1634977 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1996 NC_002945.4 1634978 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1997 NC_002945.4 1634979 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
1998 NC_002945.4 1634980 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
diff changeset
1999 NC_002945.4 1634981 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2000 NC_002945.4 1634982 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2001 NC_002945.4 1634983 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2002 NC_002945.4 1634984 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2003 NC_002945.4 1634985 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2004 NC_002945.4 1634986 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2005 NC_002945.4 1634987 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
2006 NC_002945.4 1634988 . N . . . . GT ./.
da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
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parents:
diff changeset
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da20c7c76d06 Uploaded
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parents:
diff changeset
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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da20c7c76d06 Uploaded
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parents:
diff changeset
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da20c7c76d06 Uploaded
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parents:
diff changeset
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da20c7c76d06 Uploaded
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parents:
diff changeset
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da20c7c76d06 Uploaded
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parents:
diff changeset
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da20c7c76d06 Uploaded
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parents:
diff changeset
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da20c7c76d06 Uploaded
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diff changeset
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da20c7c76d06 Uploaded
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parents:
diff changeset
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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da20c7c76d06 Uploaded
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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greg
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2907 NC_002945.4 3209298 . N . . . . GT ./.
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2912 NC_002945.4 3219356 . N . . . . GT ./.
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2916 NC_002945.4 3247623 . C T 6755.77 . AC=2;AF=1.00;AN=2;DP=234;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.25;SOR=1.234 GT:AD:DP:GQ:PL 1/1:0,231:231:99:6784,687,0
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2918 NC_002945.4 3267690 . A G 8125.77 . AC=2;AF=1.00;AN=2;DP=253;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.12;SOR=0.750 GT:AD:DP:GQ:PL 1/1:0,253:253:99:8154,753,0
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2919 NC_002945.4 3270181 . A G 9105.77 . AC=2;AF=1.00;AN=2;DP=309;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.56;SOR=0.719 GT:AD:DP:GQ:PL 1/1:0,308:308:99:9134,919,0
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2922 NC_002945.4 3329772 . C G 7731.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.925;ClippingRankSum=0.000;DP=257;ExcessHet=3.0103;FS=3.096;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=30.32;ReadPosRankSum=-0.608;SOR=0.299 GT:AD:DP:GQ:PL 1/1:1,254:255:99:7760,750,0
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2923 NC_002945.4 3338298 . C G 3356.77 . AC=2;AF=1.00;AN=2;DP=126;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;QD=27.07;SOR=1.197 GT:AD:DP:GQ:PL 1/1:0,124:124:99:3385,368,0
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2924 NC_002945.4 3371156 . A G 9051.77 . AC=2;AF=1.00;AN=2;DP=291;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.11;SOR=0.847 GT:AD:DP:GQ:PL 1/1:0,291:291:99:9080,866,0
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2925 NC_002945.4 3394764 . A G 9595.77 . AC=2;AF=1.00;AN=2;DP=330;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.26;SOR=0.769 GT:AD:DP:GQ:PL 1/1:0,328:328:99:9624,976,0
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2926 NC_002945.4 3396621 . G C 8668.77 . AC=2;AF=1.00;AN=2;DP=286;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.31;SOR=0.907 GT:AD:DP:GQ:PL 1/1:0,286:286:99:8697,854,0
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2928 NC_002945.4 3421983 . C T 5464.77 . AC=2;AF=1.00;AN=2;DP=170;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.12;SOR=2.069 GT:AD:DP:GQ:PL 1/1:0,165:165:99:5493,493,0
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2929 NC_002945.4 3428078 . C T 5462.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=4.079;ClippingRankSum=0.000;DP=218;ExcessHet=3.0103;FS=26.289;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=25.41;ReadPosRankSum=3.211;SOR=1.197 GT:AD:DP:GQ:PL 1/1:6,209:215:99:5491,562,0
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2930 NC_002945.4 3429376 . A C 5595.77 . AC=2;AF=1.00;AN=2;DP=165;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.33;SOR=1.698 GT:AD:DP:GQ:PL 1/1:0,163:163:99:5624,488,0
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2931 NC_002945.4 3439578 . G A 10250.77 . AC=2;AF=1.00;AN=2;DP=359;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.88;SOR=0.909 GT:AD:DP:GQ:PL 1/1:0,355:355:99:10279,1056,0
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2932 NC_002945.4 3450988 . C T 9125.77 . AC=2;AF=1.00;AN=2;DP=307;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.92;SOR=1.156 GT:AD:DP:GQ:PL 1/1:0,305:305:99:9154,907,0
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2933 NC_002945.4 3451869 . C A 8997.77 . AC=2;AF=1.00;AN=2;DP=317;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.66;SOR=0.706 GT:AD:DP:GQ:PL 1/1:0,314:314:99:9026,929,0
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2934 NC_002945.4 3464524 . T C 5370.77 . AC=2;AF=1.00;AN=2;DP=139;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.51;SOR=5.361 GT:AD:DP:GQ:PL 1/1:0,138:138:99:5399,414,0
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2935 NC_002945.4 3471404 . A G 11021.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.621;ClippingRankSum=0.000;DP=358;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=31.13;ReadPosRankSum=-0.717;SOR=1.272 GT:AD:DP:GQ:PL 1/1:2,352:354:99:11050,1033,0
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2936 NC_002945.4 3482644 . A T 6350.77 . AC=2;AF=1.00;AN=2;DP=220;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.27;SOR=0.861 GT:AD:DP:GQ:PL 1/1:0,217:217:99:6379,644,0
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2937 NC_002945.4 3484836 . A G 9592.77 . AC=2;AF=1.00;AN=2;DP=328;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.94;QD=29.43;SOR=0.782 GT:AD:DP:GQ:PL 1/1:0,326:326:99:9621,971,0
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2938 NC_002945.4 3495510 . C T 7253.77 . AC=2;AF=1.00;AN=2;DP=255;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.13;SOR=1.055 GT:AD:DP:GQ:PL 1/1:0,249:249:99:7282,738,0
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2939 NC_002945.4 3521264 . C T 8800.77 . AC=2;AF=1.00;AN=2;DP=309;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.57;SOR=0.774 GT:AD:DP:GQ:PL 1/1:0,308:308:99:8829,919,0
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2940 NC_002945.4 3558883 . G C 7931.77 . AC=2;AF=1.00;AN=2;DP=240;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.61;SOR=2.282 GT:AD:DP:GQ:PL 1/1:0,236:236:99:7960,702,0
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2941 NC_002945.4 3574014 . T C 9000.77 . AC=2;AF=1.00;AN=2;DP=290;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.14;SOR=1.227 GT:AD:DP:GQ:PL 1/1:0,289:289:99:9029,862,0
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2942 NC_002945.4 3577163 . G T 9642.77 . AC=2;AF=1.00;AN=2;DP=300;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.25;SOR=1.130 GT:AD:DP:GQ:PL 1/1:0,299:299:99:9671,893,0
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2943 NC_002945.4 3626128 . T C 7529.77 . AC=2;AF=1.00;AN=2;DP=239;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.51;SOR=0.826 GT:AD:DP:GQ:PL 1/1:0,239:239:99:7558,715,0
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2944 NC_002945.4 3629370 . G A 8131.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.877;ClippingRankSum=0.000;DP=278;ExcessHet=3.0103;FS=3.268;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=29.25;ReadPosRankSum=2.075;SOR=0.423 GT:AD:DP:GQ:PL 1/1:1,277:278:99:8160,818,0
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2945 NC_002945.4 3667823 . A G 10431.77 . AC=2;AF=1.00;AN=2;DP=336;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.03;QD=31.05;SOR=0.742 GT:AD:DP:GQ:PL 1/1:0,336:336:99:10460,1004,0
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2946 NC_002945.4 3695728 . N . . . . GT ./.
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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da20c7c76d06 Uploaded
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diff changeset
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greg
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3735 NC_002945.4 4294052 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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da20c7c76d06 Uploaded
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3737 NC_002945.4 4294054 . N . . . . GT ./.
da20c7c76d06 Uploaded
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3738 NC_002945.4 4294055 . N . . . . GT ./.
da20c7c76d06 Uploaded
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3739 NC_002945.4 4294056 . N . . . . GT ./.
da20c7c76d06 Uploaded
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3740 NC_002945.4 4294057 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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3741 NC_002945.4 4294058 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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3742 NC_002945.4 4294059 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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3743 NC_002945.4 4294060 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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3744 NC_002945.4 4294061 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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3745 NC_002945.4 4294062 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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3746 NC_002945.4 4294063 . N . . . . GT ./.
da20c7c76d06 Uploaded
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3747 NC_002945.4 4294064 . N . . . . GT ./.
da20c7c76d06 Uploaded
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3748 NC_002945.4 4294065 . N . . . . GT ./.
da20c7c76d06 Uploaded
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3749 NC_002945.4 4294066 . N . . . . GT ./.
da20c7c76d06 Uploaded
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3750 NC_002945.4 4294067 . N . . . . GT ./.
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3751 NC_002945.4 4294068 . N . . . . GT ./.
da20c7c76d06 Uploaded
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3752 NC_002945.4 4294069 . N . . . . GT ./.
da20c7c76d06 Uploaded
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3753 NC_002945.4 4294070 . N . . . . GT ./.
da20c7c76d06 Uploaded
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3754 NC_002945.4 4294071 . N . . . . GT ./.
da20c7c76d06 Uploaded
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3755 NC_002945.4 4294072 . N . . . . GT ./.
da20c7c76d06 Uploaded
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3756 NC_002945.4 4294073 . N . . . . GT ./.
da20c7c76d06 Uploaded
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3757 NC_002945.4 4294074 . N . . . . GT ./.
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3758 NC_002945.4 4294075 . N . . . . GT ./.
da20c7c76d06 Uploaded
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3759 NC_002945.4 4294076 . N . . . . GT ./.
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3760 NC_002945.4 4294077 . N . . . . GT ./.
da20c7c76d06 Uploaded
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parents:
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3761 NC_002945.4 4298265 . T C 5021.77 . AC=2;AF=1.00;AN=2;DP=152;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.04;SOR=0.774 GT:AD:DP:GQ:PL 1/1:0,152:152:99:5050,454,0
da20c7c76d06 Uploaded
greg
parents:
diff changeset
3762 NC_002945.4 4311302 . C T 10501.77 . AC=2;AF=1.00;AN=2;DP=348;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.18;SOR=0.740 GT:AD:DP:GQ:PL 1/1:0,348:348:99:10530,1036,0
da20c7c76d06 Uploaded
greg
parents:
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da20c7c76d06 Uploaded
greg
parents:
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da20c7c76d06 Uploaded
greg
parents:
diff changeset
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