Mercurial > repos > iuc > gvcftools_extract_variants
diff test-data/variants_output1.vcf @ 0:bf8841b0a6b0 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools commit a35519a8cc09ea0a6e6ac5f57ff36fd738e5adb7
| author | iuc |
|---|---|
| date | Mon, 20 Feb 2017 06:35:42 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/variants_output1.vcf Mon Feb 20 06:35:42 2017 -0500 @@ -0,0 +1,208 @@ +##fileformat=VCFv4.1 +##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> +##FILTER=<ID=LowQual,Description="Low quality"> +##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> +##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> +##GATKCommandLine=<ID=HaplotypeCaller,Version=3.3-0-g37228af,Date="Sun Jun 07 11:04:37 SAST 2015",Epoch=1433667877260,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[./R_2117_866#L5-_.R.bam.sorted_dedup.bam_realigned.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=reference_H37Rv.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 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 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 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 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=4 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=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=1 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=true sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false 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 minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 mergeVariantsViaLD=false doNotRunPhysicalPhasing=true pair_hmm_implementation=VECTOR_LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=1000 minReadsPerAlignmentStart=5 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null 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"> +##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive) +##GVCFBlock=minGQ=1(inclusive),maxGQ=2(exclusive) +##GVCFBlock=minGQ=10(inclusive),maxGQ=11(exclusive) +##GVCFBlock=minGQ=11(inclusive),maxGQ=12(exclusive) +##GVCFBlock=minGQ=12(inclusive),maxGQ=13(exclusive) +##GVCFBlock=minGQ=13(inclusive),maxGQ=14(exclusive) +##GVCFBlock=minGQ=14(inclusive),maxGQ=15(exclusive) +##GVCFBlock=minGQ=15(inclusive),maxGQ=16(exclusive) +##GVCFBlock=minGQ=16(inclusive),maxGQ=17(exclusive) +##GVCFBlock=minGQ=17(inclusive),maxGQ=18(exclusive) +##GVCFBlock=minGQ=18(inclusive),maxGQ=19(exclusive) +##GVCFBlock=minGQ=19(inclusive),maxGQ=20(exclusive) +##GVCFBlock=minGQ=2(inclusive),maxGQ=3(exclusive) +##GVCFBlock=minGQ=20(inclusive),maxGQ=21(exclusive) +##GVCFBlock=minGQ=21(inclusive),maxGQ=22(exclusive) +##GVCFBlock=minGQ=22(inclusive),maxGQ=23(exclusive) +##GVCFBlock=minGQ=23(inclusive),maxGQ=24(exclusive) +##GVCFBlock=minGQ=24(inclusive),maxGQ=25(exclusive) +##GVCFBlock=minGQ=25(inclusive),maxGQ=26(exclusive) +##GVCFBlock=minGQ=26(inclusive),maxGQ=27(exclusive) +##GVCFBlock=minGQ=27(inclusive),maxGQ=28(exclusive) +##GVCFBlock=minGQ=28(inclusive),maxGQ=29(exclusive) +##GVCFBlock=minGQ=29(inclusive),maxGQ=30(exclusive) +##GVCFBlock=minGQ=3(inclusive),maxGQ=4(exclusive) +##GVCFBlock=minGQ=30(inclusive),maxGQ=31(exclusive) +##GVCFBlock=minGQ=31(inclusive),maxGQ=32(exclusive) +##GVCFBlock=minGQ=32(inclusive),maxGQ=33(exclusive) +##GVCFBlock=minGQ=33(inclusive),maxGQ=34(exclusive) +##GVCFBlock=minGQ=34(inclusive),maxGQ=35(exclusive) +##GVCFBlock=minGQ=35(inclusive),maxGQ=36(exclusive) +##GVCFBlock=minGQ=36(inclusive),maxGQ=37(exclusive) +##GVCFBlock=minGQ=37(inclusive),maxGQ=38(exclusive) +##GVCFBlock=minGQ=38(inclusive),maxGQ=39(exclusive) +##GVCFBlock=minGQ=39(inclusive),maxGQ=40(exclusive) +##GVCFBlock=minGQ=4(inclusive),maxGQ=5(exclusive) +##GVCFBlock=minGQ=40(inclusive),maxGQ=41(exclusive) +##GVCFBlock=minGQ=41(inclusive),maxGQ=42(exclusive) +##GVCFBlock=minGQ=42(inclusive),maxGQ=43(exclusive) +##GVCFBlock=minGQ=43(inclusive),maxGQ=44(exclusive) +##GVCFBlock=minGQ=44(inclusive),maxGQ=45(exclusive) +##GVCFBlock=minGQ=45(inclusive),maxGQ=46(exclusive) +##GVCFBlock=minGQ=46(inclusive),maxGQ=47(exclusive) +##GVCFBlock=minGQ=47(inclusive),maxGQ=48(exclusive) +##GVCFBlock=minGQ=48(inclusive),maxGQ=49(exclusive) +##GVCFBlock=minGQ=49(inclusive),maxGQ=50(exclusive) +##GVCFBlock=minGQ=5(inclusive),maxGQ=6(exclusive) +##GVCFBlock=minGQ=50(inclusive),maxGQ=51(exclusive) +##GVCFBlock=minGQ=51(inclusive),maxGQ=52(exclusive) +##GVCFBlock=minGQ=52(inclusive),maxGQ=53(exclusive) +##GVCFBlock=minGQ=53(inclusive),maxGQ=54(exclusive) +##GVCFBlock=minGQ=54(inclusive),maxGQ=55(exclusive) +##GVCFBlock=minGQ=55(inclusive),maxGQ=56(exclusive) +##GVCFBlock=minGQ=56(inclusive),maxGQ=57(exclusive) +##GVCFBlock=minGQ=57(inclusive),maxGQ=58(exclusive) +##GVCFBlock=minGQ=58(inclusive),maxGQ=59(exclusive) +##GVCFBlock=minGQ=59(inclusive),maxGQ=60(exclusive) +##GVCFBlock=minGQ=6(inclusive),maxGQ=7(exclusive) +##GVCFBlock=minGQ=60(inclusive),maxGQ=70(exclusive) +##GVCFBlock=minGQ=7(inclusive),maxGQ=8(exclusive) +##GVCFBlock=minGQ=70(inclusive),maxGQ=80(exclusive) +##GVCFBlock=minGQ=8(inclusive),maxGQ=9(exclusive) +##GVCFBlock=minGQ=80(inclusive),maxGQ=90(exclusive) +##GVCFBlock=minGQ=9(inclusive),maxGQ=10(exclusive) +##GVCFBlock=minGQ=90(inclusive),maxGQ=99(exclusive) +##GVCFBlock=minGQ=99(inclusive),maxGQ=2147483647(exclusive) +##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> +##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> +##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> +##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> +##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> +##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"> +##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"> +##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"> +##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> +##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> +##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> +##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> +##contig=<ID=gi|448814763|ref|NC_000962.3|,length=4411532> +##reference=file:///net/datasrv3hs.sanbi.ac.za/cip0/research/scratch/zahra/TB_wrk/TB_Variant_analysis/MDR/reference_H37Rv.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ./R_2117_866#L5-_.R +gi|448814763|ref|NC_000962.3| 1977 . A G,<NON_REF> 1986 . DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,53,0:53:99:2016,0,2016:0,0,11,42 +gi|448814763|ref|NC_000962.3| 4013 . T C,<NON_REF> 2081 . DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,53,0:53:99:2111,0,2111:0,0,29,24 +gi|448814763|ref|NC_000962.3| 7362 . G C,<NON_REF> 3369 . BaseQRankSum=1.693;ClippingRankSum=1.693;DP=88;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0;MQRankSum=0.827;ReadPosRankSum=1.614 GT:AD:DP:GQ:PL:SB 1:1,87,0:88:99:3399,0,3408:0,1,40,47 +gi|448814763|ref|NC_000962.3| 7585 . G C,<NON_REF> 2294 . DP=61;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,60,0:60:99:2324,0,2324:0,0,36,24 +gi|448814763|ref|NC_000962.3| 9304 . G A,<NON_REF> 2343 . DP=69;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,69,0:69:99:2373,0,2373:0,0,31,38 +gi|448814763|ref|NC_000962.3| 11311 . A C,<NON_REF> 3627 . DP=96;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,96,0:96:99:3657,0,3657:0,0,31,65 +gi|448814763|ref|NC_000962.3| 11370 . C T,<NON_REF> 2699 . DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,77,0:77:99:2729,0,2729:0,0,21,56 +gi|448814763|ref|NC_000962.3| 11879 . A G,<NON_REF> 2659 . DP=70;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,69,0:69:99:2689,0,2689:0,0,36,33 +gi|448814763|ref|NC_000962.3| 14785 . T C,<NON_REF> 3506 . DP=90;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,90,0:90:99:3536,0,3536:0,0,38,52 +gi|448814763|ref|NC_000962.3| 21795 . G A,<NON_REF> 784 . DP=24;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,24,0:24:99:814,0,814:0,0,8,16 +gi|448814763|ref|NC_000962.3| 24698 . GCCGCGTTGCTCGGGGTAA G,<NON_REF> 1536.97 . DP=51;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.01;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,36,0:36:99:1576,0,1576:0,0,25,11 +gi|448814763|ref|NC_000962.3| 26959 . C G,<NON_REF> 2474 . DP=66;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,66,0:66:99:2504,0,2504:0,0,41,25 +gi|448814763|ref|NC_000962.3| 29482 . CA C,<NON_REF> 2528.97 . DP=74;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.14;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,72,0:72:99:2568,0,2568:0,0,34,38 +gi|448814763|ref|NC_000962.3| 30519 . C T,<NON_REF> 2289 . BaseQRankSum=1.681;ClippingRankSum=0.026;DP=68;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0;MQRankSum=-1.525;ReadPosRankSum=1.060 GT:AD:DP:GQ:PL:SB 1:1,66,0:67:99:2319,0,2329:1,0,47,19 +gi|448814763|ref|NC_000962.3| 30688 . T G,<NON_REF> 2109 . DP=56;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,56,0:56:99:2139,0,2139:0,0,30,26 +gi|448814763|ref|NC_000962.3| 30943 . C T,<NON_REF> 1534 . DP=49;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,49,0:49:99:1564,0,1564:0,0,28,21 +gi|448814763|ref|NC_000962.3| 31077 . C T,<NON_REF> 1499 . DP=43;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,43,0:43:99:1529,0,1529:0,0,24,19 +gi|448814763|ref|NC_000962.3| 32349 . CCCGCGCGTCGGCGATGCGTCGCGTCGAGTCGGCGATG C,<NON_REF> 3070.97 . DP=75;MLEAC=1,0;MLEAF=1.00,0.00;MQ=65.20;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,70,0:70:99:3110,0,3110:0,0,35,35 +gi|448814763|ref|NC_000962.3| 34044 . T C,<NON_REF> 3703 . DP=94;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,94,0:94:99:3733,0,3733:0,0,60,34 +gi|448814763|ref|NC_000962.3| 37031 . C G,<NON_REF> 1773 . DP=47;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,46,0:46:99:1803,0,1803:0,0,22,24 +gi|448814763|ref|NC_000962.3| 37910 . C A,<NON_REF> 3793 . DP=113;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,113,0:113:99:3823,0,3823:0,0,62,51 +gi|448814763|ref|NC_000962.3| 39223 . GC G,<NON_REF> 1460.97 . DP=50;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,46,0:46:99:1500,0,1500:0,0,19,27 +gi|448814763|ref|NC_000962.3| 42967 . G C,<NON_REF> 2609 . DP=67;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,67,0:67:99:2639,0,2639:0,0,15,52 +gi|448814763|ref|NC_000962.3| 50557 . T C,<NON_REF> 2896 . DP=73;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,73,0:73:99:2926,0,2926:0,0,43,30 +gi|448814763|ref|NC_000962.3| 51949 . A G,<NON_REF> 3374 . DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,76,0:76:99:3404,0,3404:0,0,33,43 +gi|448814763|ref|NC_000962.3| 51954 . T A,<NON_REF> 3329 . DP=72;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,71,0:71:99:3359,0,3359:0,0,29,42 +gi|448814763|ref|NC_000962.3| 53785 . C G,<NON_REF> 3639 . DP=96;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,96,0:96:99:3669,0,3669:0,0,54,42 +gi|448814763|ref|NC_000962.3| 54394 . A G,<NON_REF> 3218 . DP=83;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,83,0:83:99:3248,0,3248:0,0,40,43 +gi|448814763|ref|NC_000962.3| 55553 . C CCGCCGT,<NON_REF> 942.97 . DP=25;MLEAC=1,0;MLEAF=1.00,0.00;MQ=74.16;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,24,0:24:99:982,0,982:0,0,8,16 +gi|448814763|ref|NC_000962.3| 57393 . A T,<NON_REF> 1304 . DP=36;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,36,0:36:99:1334,0,1334:0,0,32,4 +gi|448814763|ref|NC_000962.3| 62049 . A G,<NON_REF> 1820 . DP=48;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,48,0:48:99:1850,0,1850:0,0,24,24 +gi|448814763|ref|NC_000962.3| 62657 . G A,<NON_REF> 3950 . DP=109;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,109,0:109:99:3980,0,3980:0,0,64,45 +gi|448814763|ref|NC_000962.3| 66285 . C G,<NON_REF> 2074 . DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,53,0:53:99:2104,0,2104:0,0,20,33 +gi|448814763|ref|NC_000962.3| 69871 . C T,<NON_REF> 3532 . DP=101;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,101,0:101:99:3562,0,3562:0,0,42,59 +gi|448814763|ref|NC_000962.3| 69989 . G A,<NON_REF> 1569 . DP=50;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,50,0:50:99:1599,0,1599:0,0,16,34 +gi|448814763|ref|NC_000962.3| 70816 . A G,<NON_REF> 3136 . DP=83;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,83,0:83:99:3166,0,3166:0,0,59,24 +gi|448814763|ref|NC_000962.3| 71336 . G C,<NON_REF> 1177 . DP=30;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,30,0:30:99:1207,0,1207:0,0,25,5 +gi|448814763|ref|NC_000962.3| 71584 . C CCGAGCGCTGTTCTGGCGCTAATCTGACGCTAGAATAG,<NON_REF> 3237.97 . DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.86;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,47,0:47:99:3277,0,3287:0,0,28,19 +gi|448814763|ref|NC_000962.3| 75264 . C T,<NON_REF> 2055 . DP=58;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,58,0:58:99:2085,0,2085:0,0,24,34 +gi|448814763|ref|NC_000962.3| 75940 . G C,<NON_REF> 2042 . DP=55;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,55,0:55:99:2072,0,2072:0,0,32,23 +gi|448814763|ref|NC_000962.3| 80616 . C G,<NON_REF> 3150 . DP=81;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,81,0:81:99:3180,0,3180:0,0,39,42 +gi|448814763|ref|NC_000962.3| 83982 . A G,<NON_REF> 3138 . DP=83;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,82,0:82:99:3168,0,3168:0,0,38,44 +gi|448814763|ref|NC_000962.3| 86576 . G A,<NON_REF> 2322 . DP=65;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,65,0:65:99:2352,0,2352:0,0,31,34 +gi|448814763|ref|NC_000962.3| 92199 . T G,<NON_REF> 697 . DP=20;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,20,0:20:99:727,0,727:0,0,15,5 +gi|448814763|ref|NC_000962.3| 95591 . G T,<NON_REF> 2735 . DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,77,0:77:99:2765,0,2765:0,0,29,48 +gi|448814763|ref|NC_000962.3| 97388 . G T,<NON_REF> 3943 . DP=114;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,113,0:113:99:3973,0,3973:0,0,57,56 +gi|448814763|ref|NC_000962.3| 103836 . G T,<NON_REF> 413 . DP=12;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.44;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,12,0:12:99:443,0,443:0,0,0,12 +gi|448814763|ref|NC_000962.3| 104712 . C T,<NON_REF> 518 . DP=15;MLEAC=1,0;MLEAF=1.00,0.00;MQ=68.35;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,15,0:15:99:548,0,548:0,0,14,1 +gi|448814763|ref|NC_000962.3| 109812 . C T,<NON_REF> 109 . BaseQRankSum=-4.970;ClippingRankSum=2.099;DP=59;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0;MQRankSum=-1.061;ReadPosRankSum=0.191 GT:AD:DP:GQ:PL:SB 1:26,33,0:59:99:139,0,1182:13,13,19,14 +gi|448814763|ref|NC_000962.3| 116000 . T G,<NON_REF> 2435 . DP=63;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,63,0:63:99:2465,0,2465:0,0,40,23 +gi|448814763|ref|NC_000962.3| 119669 . G A,<NON_REF> 3467 . DP=96;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,96,0:96:99:3497,0,3497:0,0,48,48 +gi|448814763|ref|NC_000962.3| 122109 . A G,<NON_REF> 2888 . DP=79;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,79,0:79:99:2918,0,2918:0,0,53,26 +gi|448814763|ref|NC_000962.3| 125830 . G GA,<NON_REF> 2470.97 . DP=81;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,76,0:76:99:2510,0,2510:0,0,20,56 +gi|448814763|ref|NC_000962.3| 128338 . G C,<NON_REF> 1736 . DP=45;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,45,0:45:99:1766,0,1766:0,0,24,21 +gi|448814763|ref|NC_000962.3| 131174 . T TG,<NON_REF> 2379.97 . DP=71;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,67,0:67:99:2419,0,2419:0,0,40,27 +gi|448814763|ref|NC_000962.3| 132417 . C G,<NON_REF> 490 . DP=13;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,13,0:13:99:520,0,520:0,0,1,12 +gi|448814763|ref|NC_000962.3| 133839 . C T,<NON_REF> 2631 . DP=75;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,75,0:75:99:2661,0,2661:0,0,35,40 +gi|448814763|ref|NC_000962.3| 137850 . GT G,<NON_REF> 2180.97 . DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,68,0:68:99:2220,0,2220:0,0,34,34 +gi|448814763|ref|NC_000962.3| 144390 . G A,<NON_REF> 1439 . DP=41;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,41,0:41:99:1469,0,1469:0,0,28,13 +gi|448814763|ref|NC_000962.3| 146087 . T C,<NON_REF> 2308 . DP=59;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,59,0:59:99:2338,0,2338:0,0,30,29 +gi|448814763|ref|NC_000962.3| 147985 . C T,<NON_REF> 2152 . DP=62;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,62,0:62:99:2182,0,2182:0,0,24,38 +gi|448814763|ref|NC_000962.3| 150326 . CAATCGGCCT C,<NON_REF> 140.97 . DP=4;MLEAC=1,0;MLEAF=1.00,0.00;MQ=59.60;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,4,0:4:99:180,0,180:0,0,2,2 +gi|448814763|ref|NC_000962.3| 151177 . G C,<NON_REF> 2127 . DP=56;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,56,0:56:99:2157,0,2157:0,0,37,19 +gi|448814763|ref|NC_000962.3| 154283 . T C,<NON_REF> 2901 . BaseQRankSum=1.646;ClippingRankSum=-0.909;DP=80;MLEAC=1,0;MLEAF=1.00,0.00;MQ=68.73;MQ0=0;MQRankSum=-1.213;ReadPosRankSum=1.342 GT:AD:DP:GQ:PL:SB 1:1,79,0:80:99:2931,0,2955:1,0,38,41 +gi|448814763|ref|NC_000962.3| 155293 . G A,<NON_REF> 1652 . DP=49;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,49,0:49:99:1682,0,1682:0,0,27,22 +gi|448814763|ref|NC_000962.3| 163573 . A C,<NON_REF> 1809 . DP=48;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,48,0:48:99:1839,0,1839:0,0,23,25 +gi|448814763|ref|NC_000962.3| 174684 . C A,<NON_REF> 1780 . DP=52;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,52,0:52:99:1810,0,1810:0,0,30,22 +gi|448814763|ref|NC_000962.3| 177596 . T C,<NON_REF> 2967 . DP=78;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,78,0:78:99:2997,0,2997:0,0,63,15 +gi|448814763|ref|NC_000962.3| 177857 . G A,<NON_REF> 1506 . DP=43;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,42,0:42:99:1536,0,1536:0,0,1,41 +gi|448814763|ref|NC_000962.3| 178946 . C T,<NON_REF> 1368 . DP=40;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,40,0:40:99:1398,0,1398:0,0,12,28 +gi|448814763|ref|NC_000962.3| 187584 . A G,<NON_REF> 2307 . DP=60;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,60,0:60:99:2337,0,2337:0,0,29,31 +gi|448814763|ref|NC_000962.3| 187738 . G A,<NON_REF> 2535 . DP=72;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,72,0:72:99:2565,0,2565:0,0,36,36 +gi|448814763|ref|NC_000962.3| 188800 . T C,<NON_REF> 1495 . DP=41;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,41,0:41:99:1525,0,1525:0,0,20,21 +gi|448814763|ref|NC_000962.3| 191853 . A G,<NON_REF> 2101 . DP=55;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,55,0:55:99:2131,0,2131:0,0,21,34 +gi|448814763|ref|NC_000962.3| 194681 . G C,<NON_REF> 1539 . DP=39;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,39,0:39:99:1569,0,1569:0,0,13,26 +gi|448814763|ref|NC_000962.3| 196642 . C T,<NON_REF> 4724 . DP=132;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,132,0:132:99:4754,0,4754:0,0,59,73 +gi|448814763|ref|NC_000962.3| 206339 . T C,<NON_REF> 2188 . DP=57;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,57,0:57:99:2218,0,2218:0,0,33,24 +gi|448814763|ref|NC_000962.3| 220050 . C T,<NON_REF> 981 . DP=28;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,28,0:28:99:1011,0,1011:0,0,3,25 +gi|448814763|ref|NC_000962.3| 223942 . T C,<NON_REF> 486 . DP=13;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,13,0:13:99:516,0,516:0,0,10,3 +gi|448814763|ref|NC_000962.3| 225323 . T C,<NON_REF> 2159 . DP=57;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,57,0:57:99:2189,0,2189:0,0,29,28 +gi|448814763|ref|NC_000962.3| 227098 . T C,<NON_REF> 2543 . DP=66;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,66,0:66:99:2573,0,2573:0,0,31,35 +gi|448814763|ref|NC_000962.3| 231114 . C G,<NON_REF> 4042 . DP=106;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,106,0:106:99:4072,0,4072:0,0,54,52 +gi|448814763|ref|NC_000962.3| 232574 . G T,<NON_REF> 2181 . DP=61;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,61,0:61:99:2211,0,2211:0,0,32,29 +gi|448814763|ref|NC_000962.3| 234477 . T G,<NON_REF> 329 . DP=12;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,12,0:12:99:359,0,359:0,0,8,4 +gi|448814763|ref|NC_000962.3| 234496 . C CGT,<NON_REF> 995.97 . DP=20;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,20,0:20:99:1035,0,1035:0,0,12,8 +gi|448814763|ref|NC_000962.3| 251468 . G T,<NON_REF> 2046 . DP=62;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,62,0:62:99:2076,0,2076:0,0,43,19 +gi|448814763|ref|NC_000962.3| 261869 . T C,<NON_REF> 394 . DP=11;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,11,0:11:99:424,0,424:0,0,2,9 +gi|448814763|ref|NC_000962.3| 265475 . G A,<NON_REF> 4124 . DP=114;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,114,0:114:99:4154,0,4154:0,0,48,66 +gi|448814763|ref|NC_000962.3| 265554 . A C,<NON_REF> 4281 . DP=114;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,113,0:113:99:4311,0,4311:0,0,56,57 +gi|448814763|ref|NC_000962.3| 265968 . C G,<NON_REF> 2091 . DP=54;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,54,0:54:99:2121,0,2121:0,0,22,32 +gi|448814763|ref|NC_000962.3| 278681 . C G,<NON_REF> 2284 . DP=59;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,59,0:59:99:2314,0,2314:0,0,36,23 +gi|448814763|ref|NC_000962.3| 283614 . T C,<NON_REF> 1794 . DP=47;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,47,0:47:99:1824,0,1824:0,0,30,17 +gi|448814763|ref|NC_000962.3| 284623 . G A,<NON_REF> 1019 . DP=31;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,31,0:31:99:1049,0,1049:0,0,22,9 +gi|448814763|ref|NC_000962.3| 285772 . A C,<NON_REF> 1085 . DP=28;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,28,0:28:99:1115,0,1115:0,0,11,17 +gi|448814763|ref|NC_000962.3| 285871 . A G,<NON_REF> 1112 . DP=29;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,29,0:29:99:1142,0,1142:0,0,19,10 +gi|448814763|ref|NC_000962.3| 293628 . A AC,<NON_REF> 1458.97 . DP=46;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,46,0:46:99:1498,0,1498:0,0,36,10 +gi|448814763|ref|NC_000962.3| 301290 . G A,<NON_REF> 2691 . DP=81;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,81,0:81:99:2721,0,2721:0,0,41,40 +gi|448814763|ref|NC_000962.3| 304679 . G T,<NON_REF> 3530 . DP=101;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,101,0:101:99:3560,0,3560:0,0,46,55 +gi|448814763|ref|NC_000962.3| 304923 . A G,<NON_REF> 3082 . DP=84;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,84,0:84:99:3112,0,3112:0,0,52,32 +gi|448814763|ref|NC_000962.3| 310973 . G A,<NON_REF> 1535 . DP=45;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,45,0:45:99:1565,0,1565:0,0,28,17 +gi|448814763|ref|NC_000962.3| 311613 . G T,<NON_REF> 2695 . DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,77,0:77:99:2725,0,2725:0,0,44,33 +gi|448814763|ref|NC_000962.3| 315502 . C A,<NON_REF> 1010 . DP=30;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,30,0:30:99:1040,0,1040:0,0,14,16 +gi|448814763|ref|NC_000962.3| 320038 . G A,<NON_REF> 626 . DP=19;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,19,0:19:99:656,0,656:0,0,9,10 +gi|448814763|ref|NC_000962.3| 328641 . G T,<NON_REF> 1816 . DP=51;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,51,0:51:99:1846,0,1846:0,0,17,34 +gi|448814763|ref|NC_000962.3| 335971 . A G,<NON_REF> 1022 . DP=25;MLEAC=1,0;MLEAF=1.00,0.00;MQ=63.45;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,25,0:25:99:1052,0,1052:0,0,12,13 +gi|448814763|ref|NC_000962.3| 336047 . C G,<NON_REF> 1353 . BaseQRankSum=-0.603;ClippingRankSum=-1.789;DP=57;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.67;MQ0=0;MQRankSum=1.492;ReadPosRankSum=-2.141 GT:AD:DP:GQ:PL:SB 1:14,43,0:57:99:1383,0,2013:7,7,18,25 +gi|448814763|ref|NC_000962.3| 336050 . A G,<NON_REF> 1240 . BaseQRankSum=3.331;ClippingRankSum=-0.852;DP=49;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.28;MQ0=0;MQRankSum=-0.808;ReadPosRankSum=-1.826 GT:AD:DP:GQ:PL:SB 1:14,35,0:49:99:1270,0,1900:7,7,12,23 +gi|448814763|ref|NC_000962.3| 336053 . G C,<NON_REF> 870 . BaseQRankSum=-0.454;ClippingRankSum=-0.570;DP=47;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.16;MQ0=0;MQRankSum=0.896;ReadPosRankSum=-1.780 GT:AD:DP:GQ:PL:SB 1:14,33,0:47:99:900,0,1530:7,7,11,22 +gi|448814763|ref|NC_000962.3| 336191 . C T,<NON_REF> 1569 . DP=44;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.79;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,44,0:44:99:1599,0,1599:0,0,38,6 +gi|448814763|ref|NC_000962.3| 336772 . C T,<NON_REF> 364 . DP=9;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,9,0:9:99:394,0,394:0,0,1,8 +gi|448814763|ref|NC_000962.3| 336773 . A G,<NON_REF> 364 . DP=8;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,8,0:8:99:394,0,394:0,0,1,7 +gi|448814763|ref|NC_000962.3| 336780 . G A,<NON_REF> 285 . DP=4;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,4,0:4:99:315,0,315:0,0,0,4 +gi|448814763|ref|NC_000962.3| 336781 . T C,<NON_REF> 150 . DP=3;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,3,0:3:99:180,0,180:0,0,0,3 +gi|448814763|ref|NC_000962.3| 336782 . G C,<NON_REF> 150 . DP=2;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,2,0:2:99:180,0,180:0,0,0,2 +gi|448814763|ref|NC_000962.3| 338020 . A C,<NON_REF> 45 . DP=2;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,2,0:2:75:75,0,75:0,0,2,0 +gi|448814763|ref|NC_000962.3| 338100 . T C,<NON_REF> 216 . DP=6;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.19;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,6,0:6:99:246,0,246:0,0,6,0