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roxy.vcf
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roxy.vcf
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##fileformat=VCFv4.1
##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
##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=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="RMS Mapping Quality">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=VF,Number=1,Type=Float,Description="Variant Frequency, the ratio of the sum of the called variant depth to the total depth">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=BLOCKAVG_min30p3a,Number=0,Type=Flag,Description="Non-variant site block. All sites in a block are constrained to be non-variant, have the same filter value, and have all sample values in range [x,y], y <= max(x+3,(x*1.3)). All printed site block sample values are the minimum observed in the region spanned by the block">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the region described in this record">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##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=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">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained gaussian mixture model">
##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
##FILTER=<ID=LowGQX,Description="Locus GQX is less than 30.0000 or not present">
##FILTER=<ID=LowQD,Description="Locus QD is less than 2.0000">
##FILTER=<ID=LowMQ,Description="Site MQ is less than 20.0000">
##FILTER=<ID=IndelConflict,Description="Locus is in region with conflicting indel calls.">
##FILTER=<ID=MaxDepth,Description="Site depth is greater than 3.0x the mean chromosome depth">
##FILTER=<ID=SiteConflict,Description="Site genotype conflicts with proximal indel call. This is typically a heterozygous SNV call made inside of a heterozygous deletion.">
##FILTER=<ID=TruthSensitivityTranche99.00to99.90,Description="Truth sensitivity tranche level at VSQ Lod: -1.8667 <= x < -0.5971">
##FILTER=<ID=TruthSensitivityTranche99.90to100.00+,Description="Truth sensitivity tranche level at VQS Lod < -110.8111">
##FILTER=<ID=TruthSensitivityTranche99.90to100.00,Description="Truth sensitivity tranche level at VSQ Lod: -110.8111 <= x < -1.8667">
##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] read_buffer_size=null phone_home=NO_ET gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFASTA/genome.fa nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=-1 defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false input=[(RodBinding name=input source=/illumina/builds/platinumgenomes/Platinum_Genomes_Short_Insert/bwa_0.6.1/NA12878/Data/Intensities/BaseCalls/Alignment/tempvariants_G1.1.Indel.txt)] recal_file=(RodBinding name=recal_file source=/illumina/builds/platinumgenomes/Platinum_Genomes_Short_Insert/bwa_0.6.1/NA12878/Data/Intensities/BaseCalls/Alignment/tempvariants_G1.1.vcf.1.recal) tranches_file=/illumina/builds/platinumgenomes/Platinum_Genomes_Short_Insert/bwa_0.6.1/NA12878/Data/Intensities/BaseCalls/Alignment/tempvariants_G1.1.vcf.1.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=99.0 ignore_filter=null mode=INDEL filter_mismatching_base_and_quals=false"
##CombineVariants="analysis_type=CombineVariants input_file=[] read_buffer_size=null phone_home=NO_ET gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFASTA/genome.fa nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=-1 defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false variant=[(RodBinding name=variant source=/illumina/builds/platinumgenomes/Platinum_Genomes_Short_Insert/bwa_0.6.1/NA12878/Data/Intensities/BaseCalls/Alignment/tempvariants_G1.1.vcf.0.output), (RodBinding name=variant2 source=/illumina/builds/platinumgenomes/Platinum_Genomes_Short_Insert/bwa_0.6.1/NA12878/Data/Intensities/BaseCalls/Alignment/tempvariants_G1.1.vcf.1.output)] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=variant2,variant printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_mismatching_base_and_quals=false"
##MaxDepth_chr10=163.71
##MaxDepth_chr11=151.44
##MaxDepth_chr12=152.01
##MaxDepth_chr13=128.88
##MaxDepth_chr14=128.73
##MaxDepth_chr15=123.54
##MaxDepth_chr16=152.97
##MaxDepth_chr17=150.36
##MaxDepth_chr18=152.97
##MaxDepth_chr19=147.24
##MaxDepth_chr1=149.37
##MaxDepth_chr20=146.76
##MaxDepth_chr21=127.47
##MaxDepth_chr22=103.2
##MaxDepth_chr2=157.56
##MaxDepth_chr3=155.01
##MaxDepth_chr4=154.92
##MaxDepth_chr5=154.65
##MaxDepth_chr6=155.97
##MaxDepth_chr7=154.8
##MaxDepth_chr8=154.44
##MaxDepth_chr9=136.53
##MaxDepth_chrM=60475.3
##MaxDepth_chrX=150.15
##MaxDepth_chrY=9.87
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/illumina/builds/platinumgenomes/Platinum_Genomes_Short_Insert/bwa_0.6.1/NA12878/Data/Intensities/BaseCalls/Alignment/NA12878_S1.bam] read_buffer_size=null phone_home=NO_ET gatk_key=null read_filter=[] intervals=[chrM:1-16571] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFASTA/genome.fa nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=-1 defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=OFF log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=1.0 standard_min_confidence_threshold_for_emitting=30.0 noSLOD=false annotateNDA=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 max_alternate_alleles=3 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 noBandedIndel=false indelDebug=false ignoreSNPAlleles=false includeGVCFData=true dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig=<ID=chr1,length=249250621>
##contig=<ID=chr10,length=135534747>
##contig=<ID=chr11,length=135006516>
##contig=<ID=chr12,length=133851895>
##contig=<ID=chr13,length=115169878>
##contig=<ID=chr14,length=107349540>
##contig=<ID=chr15,length=102531392>
##contig=<ID=chr16,length=90354753>
##contig=<ID=chr17,length=81195210>
##contig=<ID=chr18,length=78077248>
##contig=<ID=chr19,length=59128983>
##contig=<ID=chr2,length=243199373>
##contig=<ID=chr20,length=63025520>
##contig=<ID=chr21,length=48129895>
##contig=<ID=chr22,length=51304566>
##contig=<ID=chr3,length=198022430>
##contig=<ID=chr4,length=191154276>
##contig=<ID=chr5,length=180915260>
##contig=<ID=chr6,length=171115067>
##contig=<ID=chr7,length=159138663>
##contig=<ID=chr8,length=146364022>
##contig=<ID=chr9,length=141213431>
##contig=<ID=chrM,length=16571>
##contig=<ID=chrX,length=155270560>
##contig=<ID=chrY,length=59373566>
##gvcftools_cmdline="/illumina/development/Isis/2.2.13/gatk_to_gvcf --chrom-depth-file=/illumina/builds/platinumgenomes/Platinum_Genomes_Short_Insert/bwa_0.6.1/NA12878/Data/Intensities/BaseCalls/Alignment/NA12878_S1.bam.depth --no-default-filters --min-qd 2.0000 --min-gqx 30.0000 --min-mq 20.0000"
##gvcftools_version="v0.8"
##reference=file:///illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFASTA/genome.fa
##source=GATK 1.6
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr17 41199659 rs80358145 C T . . . . 0/1:242:99:42
chrM 1 . G . . PASS . GT:DP:GQX:MQ 0/0:147:99:49
chrM 2 . A . . PASS END=72;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:42
chrM 73 . G A 8752.78 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=50;MQ0=0;QD=35.01;SB=-4310.52;VQSLOD=-46.8060;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:50:8753,740,0:1.000
chrM 74 . T . . PASS END=149;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:46
chrM 150 . T C 9341.36 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=50;MQ0=0;QD=37.37;SB=-4089.46;VQSLOD=-46.3916;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:50:9341,749,0:1.000
chrM 151 . C . . PASS . GT:DP:GQX:MQ 0/0:250:99:50
chrM 152 . T C 9463.81 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=1.3990;MQ=51;MQ0=0;QD=37.86;SB=-4617.60;VQSLOD=-44.8775;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:51:9464,752,0:1.000
chrM 153 . A . . PASS END=194;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:49
chrM 195 . C T 9426.61 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=1.5661;MQ=53;MQ0=0;QD=37.71;SB=-4602.70;VQSLOD=-46.0789;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:53:9427,752,0:1.000
chrM 196 . T . . PASS END=301;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:51
chrM 302 . A C 839.83 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=-2.019;DP=250;DS;Dels=0.00;FS=142.285;HRun=8;HaplotypeScore=33.1364;MQ=54;MQ0=0;MQRankSum=3.110;QD=3.36;ReadPosRankSum=-3.951;SB=-0.01;VQSLOD=-53.2044;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:170,78:250:99:99:54:870,0,3332:0.315
chrM 303 . C . . PASS END=409;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:52
chrM 410 . A T 9036.02 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=1.663;DP=250;DS;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=8.1849;MQ=59;MQ0=0;MQRankSum=1.384;QD=36.14;ReadPosRankSum=-0.146;SB=-4391.55;VQSLOD=-44.7831;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:1,248:250:99:99:59:9036,731,0:0.996
chrM 411 . G . . PASS END=1020;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:246:99:51
chrM 1021 . A . . PASS END=1107;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:34
chrM 1108 . C . . PASS END=1185;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:29
chrM 1186 . T . . PASS END=1576;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:246:99:46
chrM 1577 . T . . PASS END=2260;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:56
chrM 2261 . C T 9223.24 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=59;MQ0=0;QD=36.89;SB=-4048.78;VQSLOD=-45.0775;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:59:9223,743,0:1.000
chrM 2262 . A . . PASS END=2353;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:58
chrM 2354 . C T 9470.86 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=5.2719;MQ=59;MQ0=0;QD=37.88;SB=-2180.88;VQSLOD=-45.2136;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,248:250:99:99:59:9471,740,0:1.000
chrM 2355 . A . . PASS END=2445;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:57
chrM 2446 . A . . PASS END=2459;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:43
chrM 2460 . A . . PASS END=2484;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:56
chrM 2485 . C T 7706.01 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=11.0166;MQ=58;MQ0=0;QD=30.82;SB=-2278.50;VQSLOD=-44.0411;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,249:250:99:99:58:7706,670,0:1.000
chrM 2486 . C . . PASS END=2488;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:58
chrM 2489 . A C 1686.66 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=-9.086;DP=250;DS;Dels=0.00;FS=323.802;HRun=4;HaplotypeScore=7.1572;MQ=58;MQ0=0;MQRankSum=3.066;QD=6.75;ReadPosRankSum=-7.145;SB=-1.87;VQSLOD=-125.9223;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:128,121:250:99:99:58:1717,0,3475:0.486
chrM 2490 . C . . PASS END=2707;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:247:99:57
chrM 2708 . G A 9063.90 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=3.7799;MQ=59;MQ0=0;QD=36.26;SB=-3802.88;VQSLOD=-44.9719;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:59:9064,734,0:1.000
chrM 2709 . A . . PASS END=3483;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:58
chrM 3484 . G C 231.71 TruthSensitivityTranche99.90to100.00;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-6.359;DP=250;DS;Dels=0.00;FS=147.254;HRun=4;HaplotypeScore=94.9439;MQ=59;MQ0=0;MQRankSum=-0.411;QD=0.93;ReadPosRankSum=-7.964;SB=-0.01;VQSLOD=-54.3182;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:201,49:250:99:99:59:262,0,5110:0.196
chrM 3485 . C . . PASS END=3492;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:59
chrM 3493 . A C 363.66 TruthSensitivityTranche99.90to100.00;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-6.883;DP=250;DS;Dels=0.00;FS=194.835;HRun=3;HaplotypeScore=7.8854;MQ=59;MQ0=0;MQRankSum=0.027;QD=1.45;ReadPosRankSum=-2.216;SB=-0.01;VQSLOD=-65.8719;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:188,62:250:99:99:59:394,0,5209:0.248
chrM 3494 . C . . PASS END=3914;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:247:99:54
chrM 3915 . G . . PASS END=3948;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:37
chrM 3949 . A . . PASS END=4105;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:247:99:47
chrM 4106 . A . . PASS END=4147;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:34
chrM 4148 . C . . PASS END=4188;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:26
chrM 4189 . A . . PASS END=4212;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:22
chrM 4213 . A . . PASS END=4226;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:36
chrM 4227 . T . . PASS END=4319;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:41
chrM 4320 . C . . PASS END=4356;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:29
chrM 4357 . C . . PASS END=4457;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:34
chrM 4458 . C . . PASS END=4552;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:25
chrM 4553 . T . . PASS END=4636;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:23
chrM 4637 . C . . PASS END=4738;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:36
chrM 4739 . C . . PASS END=4745;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:32
chrM 4746 . A G 6029.38 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=4.4245;MQ=32;MQ0=35;QD=24.12;SB=-2013.52;VQSLOD=-48.3470;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:32:6029,541,0:1.000
chrM 4747 . T . . PASS END=4756;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:30
chrM 4757 . T . . PASS END=4806;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:37
chrM 4807 . T . . PASS END=5042;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:46
chrM 5043 . A . . PASS END=5047;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:38
chrM 5048 . T . . PASS END=5149;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:47
chrM 5150 . C . . PASS END=5208;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:35
chrM 5209 . A C 201.02 TruthSensitivityTranche99.90to100.00;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-5.257;DP=250;DS;Dels=0.00;FS=156.607;HRun=3;HaplotypeScore=4.6550;MQ=35;MQ0=10;MQRankSum=-2.444;QD=0.80;ReadPosRankSum=-6.450;SB=-0.01;VQSLOD=-60.0962;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:196,53:250:99:99:35:231,0,4348:0.213
chrM 5210 . C . . PASS END=5220;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:32
chrM 5221 . C . . PASS END=5320;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:43
chrM 5321 . C . . PASS END=5499;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:44
chrM 5500 . C . . PASS END=5580;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:29
chrM 5581 . C T 6506.12 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=29;MQ0=38;QD=26.02;SB=-2473.55;VQSLOD=-48.8423;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:1,249:250:99:99:29:6506,568,0:0.996
chrM 5582 . A . . PASS END=5686;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:23
chrM 5687 . A . . PASS END=5705;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:21
chrM 5706 . A . . PASS . GT:DP:GQX:MQ 0/0:250:48:22
chrM 5707 . C . . PASS END=5721;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:20
chrM 5722 . T . . PASS END=5734;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:32
chrM 5735 . T C 629.61 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=-8.662;DP=250;DS;Dels=0.00;FS=263.754;HRun=3;HaplotypeScore=20.9043;MQ=35;MQ0=30;MQRankSum=1.753;QD=2.52;ReadPosRankSum=-4.260;SB=-0.01;VQSLOD=-95.8579;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:187,63:250:99:99:35:660,0,3523:0.252
chrM 5736 . C . . PASS END=5740;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:30
chrM 5741 . C . . PASS END=5746;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:37
chrM 5747 . G A 154.84 TruthSensitivityTranche99.90to100.00;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-7.164;DP=250;DS;Dels=0.00;FS=43.068;HRun=6;HaplotypeScore=22.8341;MQ=37;MQ0=32;MQRankSum=-3.118;QD=0.62;ReadPosRankSum=-5.711;SB=-0.01;VQSLOD=-46.5773;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:205,44:250:99:99:37:185,0,4730:0.177
chrM 5748 . A . . PASS END=5818;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:36
chrM 5819 . C . . PASS END=5841;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:38
chrM 5842 . T . . PASS END=5898;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:26
chrM 5899 . C . . PASS END=5923;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:23
chrM 5924 . T . . PASS END=5983;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:35
chrM 5984 . G . . PASS END=6024;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:44
chrM 6025 . C . . PASS END=6098;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:30
chrM 6099 . A . . PASS END=6121;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:26
chrM 6122 . T . . PASS END=6170;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:39
chrM 6171 . C . . PASS END=6419;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:50
chrM 6420 . A C 28.95 TruthSensitivityTranche99.90to100.00;LowGQX;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-7.710;DP=250;DS;Dels=0.00;FS=120.728;HRun=5;HaplotypeScore=5.7438;MQ=56;MQ0=1;MQRankSum=3.667;QD=0.12;ReadPosRankSum=-2.981;SB=-0.01;VQSLOD=-50.2113;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:202,47:250:58.93:29:56:59,0,5953:0.189
chrM 6421 . C . . PASS END=6690;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:50
chrM 6691 . G . . PASS END=6761;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:33
chrM 6762 . C . . PASS END=6835;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:27
chrM 6836 . T . . PASS END=6909;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:40
chrM 6910 . G . . PASS END=6936;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:48
chrM 6937 . A . . PASS END=7008;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:30
chrM 7009 . G . . PASS END=7028;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:26
chrM 7029 . T C 6495.30 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=2.425;DP=250;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=4.6733;MQ=27;MQ0=49;MQRankSum=-2.364;QD=25.98;ReadPosRankSum=-1.545;SB=-2887.50;VQSLOD=-49.2150;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:2,248:250:99:99:27:6495,596,0:0.992
chrM 7030 . C . . PASS END=7046;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:24
chrM 7047 . A . . PASS END=7215;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:37
chrM 7216 . C . . PASS END=7287;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:247:99:41
chrM 7288 . C . . PASS END=7298;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:31
chrM 7299 . A . . PASS END=7317;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:247:99:41
chrM 7318 . A . . PASS END=7337;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:29
chrM 7338 . G A 5650.40 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=3.4137;MQ=29;MQ0=14;QD=22.60;SB=-2621.00;VQSLOD=-48.9359;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:29:5650,523,0:1.000
chrM 7339 . A . . PASS END=7421;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:24
chrM 7422 . A . . PASS END=7522;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:41
chrM 7523 . T . . PASS END=7550;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:31
chrM 7551 . C . . PASS END=7630;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:39
chrM 7631 . T . . PASS END=7706;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:45
chrM 7707 . G . . PASS END=7711;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:37
chrM 7712 . T . . PASS END=7913;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:45
chrM 7914 . T . . PASS END=7921;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:39
chrM 7922 . C . . PASS END=8204;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:247:99:48
chrM 8205 . A . . PASS END=8275;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:34
chrM 8276 . C . . PASS END=8292;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:30
chrM 8293 . G . . PASS END=8541;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:44
chrM 8542 . G . . PASS END=8546;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:43
chrM 8547 . C . . PASS END=8556;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:33
chrM 8557 . T . . PASS END=8577;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:41
chrM 8578 . A C 7.87 TruthSensitivityTranche99.90to100.00;LowGQX;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-4.780;DP=249;DS;Dels=0.00;FS=81.593;HRun=3;HaplotypeScore=12.3727;MQ=46;MQ0=6;MQRankSum=2.388;QD=0.03;ReadPosRankSum=-5.516;SB=-0.01;VQSLOD=-47.1319;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:210,38:249:37.09:8:46:37,0,4770:0.153
chrM 8579 . C . . PASS END=8701;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:49
chrM 8702 . G A 9094.23 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=3.6910;MQ=52;MQ0=0;QD=36.38;SB=-3862.16;VQSLOD=-46.4414;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,249:250:99:99:52:9094,743,0:1.000
chrM 8703 . C . . PASS END=8719;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:51
chrM 8720 . G . . PASS END=8790;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:31
chrM 8791 . G . . PASS END=8843;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:26
chrM 8844 . T . . PASS END=8944;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:40
chrM 8945 . A . . PASS END=8960;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:34
chrM 8961 . A . . PASS END=9244;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:43
chrM 9245 . C . . PASS END=9326;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:52
chrM 9327 . A . . PASS END=9376;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:32
chrM 9377 . G . . PASS . GT:DP:GQX:MQ 0/0:250:99:31
chrM 9378 . G A 6223.59 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=32;MQ0=7;QD=24.89;SB=-2830.08;VQSLOD=-48.8304;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:32:6224,571,0:1.000
chrM 9379 . T . . PASS END=9540;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:45
chrM 9541 . C T 8790.76 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=5.2493;MQ=57;MQ0=0;QD=35.16;SB=-3609.82;VQSLOD=-45.5289;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,249:250:99:99:57:8791,731,0:1.000
chrM 9542 . T . . PASS END=9630;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:49
chrM 9631 . G . . PASS END=9656;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:36
chrM 9657 . T . . PASS END=10277;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:52
chrM 10278 . A C 313.51 TruthSensitivityTranche99.90to100.00;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-9.971;DP=250;DS;Dels=0.00;FS=186.388;HRun=4;HaplotypeScore=26.7126;MQ=60;MQ0=0;MQRankSum=-1.751;QD=1.25;ReadPosRankSum=-1.493;SB=-0.01;VQSLOD=-62.2860;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:186,63:250:99:99:60:344,0,5806:0.253
chrM 10279 . C . . PASS END=10306;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:59
chrM 10307 . A . 83.76 PASS DP=250;DS;MQ=60;MQ0=0 GT:AD:DP:GQ:MQ:GQX 0/0:187:250:53.77:60:54
chrM 10308 . C . . PASS END=10398;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:59
chrM 10399 . G A 9468.69 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.7340;MQ=60;MQ0=0;QD=37.87;SB=-2966.92;VQSLOD=-44.7803;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:60:9469,746,0:1.000
chrM 10400 . C . . PASS END=10819;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:59
chrM 10820 . G A 9212.91 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=-1.358;DP=250;DS;Dels=0.00;FS=3.540;HRun=5;HaplotypeScore=5.5453;MQ=59;MQ0=0;MQRankSum=1.690;QD=36.85;ReadPosRankSum=0.887;SB=-4025.89;VQSLOD=-43.8378;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:1,249:250:99:99:59:9213,707,0:0.996
chrM 10821 . C . . PASS END=10873;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:59
chrM 10874 . C T 8959.15 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=60;MQ0=0;QD=35.84;SB=-3958.18;VQSLOD=-44.3618;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:60:8959,740,0:1.000
chrM 10875 . C . . PASS END=10979;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:58
chrM 10980 . C . . PASS END=10984;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:45
chrM 10985 . C . . PASS END=11017;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:59
chrM 11018 . C T 9188.62 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=249;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=5.5126;MQ=59;MQ0=0;QD=36.90;SB=-2661.49;VQSLOD=-44.7389;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,249:249:99:99:59:9189,737,0:1.000
chrM 11019 . G . . PASS END=11663;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:58
chrM 11664 . C . . PASS END=11669;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:45
chrM 11670 . C . . PASS END=11719;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:59
chrM 11720 . A G 9554.66 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.0000;MQ=59;MQ0=0;QD=38.22;SB=-4260.05;VQSLOD=-44.9293;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:59:9555,749,0:1.000
chrM 11721 . C . . PASS END=11722;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:59
chrM 11723 . C T 9455.55 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=1.718;DP=250;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=5.4857;MQ=59;MQ0=0;MQRankSum=1.690;QD=37.82;ReadPosRankSum=-0.083;SB=-4388.53;VQSLOD=-44.9202;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:1,249:250:99:99:59:9456,746,0:0.996
chrM 11724 . A . . PASS END=12705;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:247:99:58
chrM 12706 . T C 9359.16 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=249;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.7333;MQ=59;MQ0=0;QD=37.59;SB=-3978.96;VQSLOD=-44.4122;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,249:249:99:99:59:9359,746,0:1.000
chrM 12707 . T . . PASS END=12850;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:246:99:59
chrM 12851 . G A 9339.82 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=2.9622;MQ=60;MQ0=0;QD=37.36;SB=-2759.31;VQSLOD=-45.0909;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:60:9340,749,0:1.000
chrM 12852 . T . . PASS END=13326;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:59
chrM 13327 . T C 8481.47 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=-0.734;DP=250;DS;Dels=0.00;FS=3.909;HRun=0;HaplotypeScore=3.4644;MQ=60;MQ0=0;MQRankSum=-0.485;QD=33.93;ReadPosRankSum=-0.125;SB=-3700.43;VQSLOD=-43.3820;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:1,249:250:99:99:60:8481,705,0:0.996
chrM 13328 . A . . PASS END=13680;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:59
chrM 13681 . C T 8824.67 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=4.4127;MQ=60;MQ0=0;QD=35.30;SB=-3019.95;VQSLOD=-44.2859;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:60:8825,746,0:1.000
chrM 13682 . A . . PASS END=14173;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:58
chrM 14174 . T . . PASS END=14175;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:45
chrM 14176 . C . . PASS END=14212;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:49
chrM 14213 . C T 9095.21 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=3.9354;MQ=59;MQ0=0;QD=36.38;SB=-4265.45;VQSLOD=-44.7911;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:59:9095,746,0:1.000
chrM 14214 . A . . PASS END=14570;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:247:99:58
chrM 14571 . C . . PASS END=14580;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:43
chrM 14581 . G A 9250.42 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=1.413;DP=250;DS;Dels=0.00;FS=3.988;HRun=1;HaplotypeScore=3.3108;MQ=58;MQ0=0;MQRankSum=-1.109;QD=37.00;ReadPosRankSum=-0.249;SB=-3682.24;VQSLOD=-43.1798;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:1,249:250:99:99:58:9250,711,0:0.996
chrM 14582 . T . . PASS END=14766;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:57
chrM 14767 . T C 9252.74 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.5779;MQ=60;MQ0=0;QD=37.01;SB=-3173.60;VQSLOD=-44.8088;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:60:9253,746,0:1.000
chrM 14768 . T . . PASS END=14831;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:247:99:58
chrM 14832 . G A 8966.50 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.3346;MQ=59;MQ0=0;QD=35.87;SB=-4129.37;VQSLOD=-44.7890;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,249:249:99:99:59:8966,734,0:1.000
chrM 14833 . C . . PASS END=14872;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:58
chrM 14873 . C T 9339.53 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=1.718;DP=250;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=3.3586;MQ=58;MQ0=0;MQRankSum=1.690;QD=37.36;ReadPosRankSum=-1.189;SB=-3590.35;VQSLOD=-45.6266;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:1,248:250:99:99:58:9340,746,0:0.996
chrM 14874 . C . . PASS END=14905;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:58
chrM 14906 . A G 9057.05 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=6.7931;MQ=59;MQ0=0;QD=36.23;SB=-3840.11;VQSLOD=-44.5729;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:59:9057,734,0:1.000
chrM 14907 . C . . PASS END=15301;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:247:99:58
chrM 15302 . A G 9050.75 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=248;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.5661;MQ=59;MQ0=0;QD=36.49;SB=-4176.90;VQSLOD=-44.2085;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,248:248:99:99:59:9051,725,0:1.000
chrM 15303 . C . . PASS END=15932;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:58
chrM 15933 . C T 9299.95 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=5.2413;MQ=58;MQ0=0;QD=37.20;SB=-3650.73;VQSLOD=-45.3149;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:58:9300,743,0:1.000
chrM 15934 . G . . PASS END=16023;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:57
chrM 16024 . G A 5431.21 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=0.884;DP=248;DS;Dels=0.00;FS=5.197;HRun=0;HaplotypeScore=0.7340;MQ=59;MQ0=0;MQRankSum=0.428;QD=21.90;ReadPosRankSum=-0.058;SB=-1562.64;VQSLOD=-43.2261;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:83,165:248:99:99:59:5431,0,2314:0.665
chrM 16025 . T . . PASS END=16172;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:47
chrM 16173 . C T 8256.98 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=1.273;DP=249;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=5.3763;MQ=56;MQ0=0;MQRankSum=1.426;QD=33.16;ReadPosRankSum=0.104;SB=-1971.54;VQSLOD=-44.6654;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:1,248:249:99:99:56:8257,709,0:0.996
chrM 16174 . C . . PASS END=16180;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:49
chrM 16181 . A C 2395.88 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=-6.520;DP=250;DS;Dels=0.00;FS=160.492;HRun=1;HaplotypeScore=180.6319;MQ=55;MQ0=0;MQRankSum=5.183;QD=9.58;ReadPosRankSum=-13.125;SB=-0.01;VQSLOD=-71.3682;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:158,91:250:99:99:55:2426,0,4900:0.365
chrM 16182 . A . . PASS END=16183;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:57
chrM 16183 . AC A 5681.26 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=1.305;DP=250;DS;FS=7.978;HRun=12;HaplotypeScore=2315.2856;MQ=57;MQ0=0;MQRankSum=1.610;QD=22.73;ReadPosRankSum=-1.335;SB=-1172.26;VQSLOD=-3.0062;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:167,82:250:99:99:57:5681,664,0:0.329
chrM 16184 . C A . LowGQX DP=250;DS;Dels=0.33;FS=0.000;HRun=3;HaplotypeScore=100.7787;MQ=57;MQ0=0;QD=16.27;SB=-306.28 GT:AD:DP:MQ .:1,167:168:57
chrM 16185 . C A 6006.09 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=-3.627;DP=250;DS;Dels=0.00;FS=5.289;HRun=0;HaplotypeScore=96.9691;MQ=57;MQ0=0;MQRankSum=3.520;QD=24.02;ReadPosRankSum=-1.232;SB=-2698.66;VQSLOD=-45.9924;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:20,228:250:57.97:58:57:6006,58,0:0.919
chrM 16186 . C . . PASS END=16190;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:250:99:50
chrM 16191 . C T 7167.26 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=0.448;DP=250;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=91.7352;MQ=57;MQ0=0;MQRankSum=1.658;QD=28.67;ReadPosRankSum=0.322;SB=-3083.90;VQSLOD=-44.5397;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:10,238:250:99:99:57:7167,375,0:0.960
chrM 16192 . C . . PASS END=16224;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:56
chrM 16225 . T C 9097.99 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=5.7340;MQ=58;MQ0=0;QD=36.39;SB=-3386.20;VQSLOD=-44.7086;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,248:250:99:99:58:9098,740,0:1.000
chrM 16226 . T . . PASS END=16321;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:53
chrM 16322 . T C 9362.60 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=1.6208;MQ=54;MQ0=0;QD=37.45;SB=-3837.44;VQSLOD=-45.5538;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,250:250:99:99:54:9363,749,0:1.000
chrM 16323 . C . . PASS END=16505;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:42
chrM 16506 . G . . PASS END=16520;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:249:99:41
chrM 16521 . C T 8635.30 TruthSensitivityTranche99.90to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=1.661;DP=248;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=14.0066;MQ=41;MQ0=0;MQRankSum=1.548;QD=34.82;ReadPosRankSum=0.511;SB=-3964.82;VQSLOD=-47.0373;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:1,243:247:99:99:41:8635,707,0:0.996
chrM 16522 . C . . PASS END=16570;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:222:99:37
chrM 16571 . G . . PASS . GT:DP:GQX:MQ 0/0:179:99:34
chr1 10001 . T . . LowMQ . GT:DP:GQX:MQ 0/0:81:48:14
chr1 10002 . A C 28.86 TruthSensitivityTranche99.90to100.00;LowGQX;LowMQ;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-0.928;DP=152;Dels=0.00;FS=35.884;HRun=0;HaplotypeScore=14.2043;MQ=12;MQ0=99;MQRankSum=2.225;QD=0.19;ReadPosRankSum=3.276;SB=-2.50;VQSLOD=-23.4292;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:146,4:152:58.85:29:12:59,0,499:0.027
chr1 10003 . A . . LowGQX;MaxDepth;LowMQ . GT:DP:GQX:MQ 0/0:199:0:13
chr1 10004 . C . . MaxDepth;LowMQ END=10014;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:247:99:13
chr1 10015 . A . . MaxDepth;LowMQ END=10024;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:17
chr1 10025 . T . . MaxDepth END=10039;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:248:99:20
chr1 10040 . C . . MaxDepth;LowMQ . GT:DP:GQX:MQ 0/0:249:99:19
chr1 10041 . C . . MaxDepth . GT:DP:GQX:MQ 0/0:250:99:20
chr1 10042 . C . . MaxDepth;LowMQ END=10083;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:247:99:19
chr1 10084 . C . . MaxDepth END=10108;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:195:99:20
chr1 10109 . A T 486.84 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=0.344;DP=198;DS;Dels=0.01;FS=20.085;HRun=0;HaplotypeScore=95.3595;MQ=21;MQ0=45;MQRankSum=-3.124;QD=2.46;ReadPosRankSum=-1.191;SB=-128.56;VQSLOD=-33.7524;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:116,73:195:99:99:21:517,0,1096:0.386
chr1 10110 . A . . MaxDepth END=10146;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:171:99:20
chr1 10147 . C . 26.74 LowGQX DP=187;DS;MQ=21;MQ0=27 GT:AD:DP:GQ:MQ:GQX 0/0:118:137:1.68:21:2
chr1 10148 . C . . MaxDepth END=10174;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:206:81:20
chr1 10175 . T . . MaxDepth;LowMQ END=10176;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:234:99:19
chr1 10177 . A C 613.36 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=4.193;DP=246;DS;Dels=0.03;FS=4.277;HRun=2;HaplotypeScore=242.8776;MQ=20;MQ0=32;MQRankSum=1.768;QD=2.49;ReadPosRankSum=-1.412;SB=-315.49;VQSLOD=-78.1557;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:172,67:239:99:99:20:643,0,1287:0.280
chr1 10177 . A AC 1842.87 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=-1.244;DP=246;DS;FS=42.087;HRun=2;HaplotypeScore=1073.8095;MQ=20;MQ0=32;MQRankSum=0.187;QD=7.49;ReadPosRankSum=0.123;SB=-123.41;VQSLOD=-5.2806;culprit=FS;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:135,102:106:99:99:20:1882,0,300:0.430
chr1 10178 . C . . MaxDepth END=10179;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:243:99:20
chr1 10180 . T C 19.06 TruthSensitivityTranche99.90to100.00;LowGQX;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=1.551;DP=249;DS;Dels=0.03;FS=6.379;HRun=2;HaplotypeScore=231.6662;MQ=20;MQ0=31;MQRankSum=-0.305;QD=0.08;ReadPosRankSum=-0.953;SB=-0.01;VQSLOD=-76.9487;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:202,36:241:49:19:20:49,0,2005:0.151
chr1 10181 . A . . MaxDepth END=10228;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:201:99:20
chr1 10229 . A . . MaxDepth END=10230;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:183:99:22
chr1 10230 . AC A 1065.12 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=-2.685;DP=185;DS;FS=2.133;HRun=4;HaplotypeScore=1144.2827;MQ=22;MQ0=27;MQRankSum=-0.693;QD=5.76;ReadPosRankSum=-0.238;SB=-419.30;VQSLOD=-2.5503;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:129,48:92:99:99:22:1104,0,588:0.271
chr1 10231 . C . 87.71 PASS DP=179;DS;MQ=21;MQ0=26 GT:AD:DP:GQ:MQ:GQX 0:119:128:57.72:21:58
chr1 10232 . C . . MaxDepth END=10233;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:162:99:22
chr1 10234 . C T 278.34 TruthSensitivityTranche99.90to100.00;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-2.340;DP=154;DS;Dels=0.03;FS=0.000;HRun=1;HaplotypeScore=152.6194;MQ=22;MQ0=20;MQRankSum=1.136;QD=1.81;ReadPosRankSum=2.464;SB=-153.76;VQSLOD=-32.5037;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:126,24:150:99:99:22:308,0,1467:0.160
chr1 10235 . T . . LowGQX . GT:DP:GQX:MQ 0/0:149:0:22
chr1 10236 . A . . MaxDepth . GT:DP:GQX:MQ 0/0:154:99:22
chr1 10237 . A . . MaxDepth . GT:DP:GQX:MQ 0/0:153:57:21
chr1 10238 . C . . MaxDepth END=10240;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:151:99:21
chr1 10241 . T . . PASS END=10246;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:139:99:22
chr1 10247 . T . . LowGQX . GT:DP:GQX:MQ 0/0:127:2:22
chr1 10248 . A T 187.69 TruthSensitivityTranche99.90to100.00;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-1.650;DP=126;DS;Dels=0.11;FS=1.496;HRun=1;HaplotypeScore=169.0619;MQ=22;MQ0=13;MQRankSum=1.432;QD=1.49;ReadPosRankSum=1.732;SB=-97.13;VQSLOD=-29.5184;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:90,20:112:99:99:22:218,0,1055:0.182
chr1 10249 . A . . PASS . GT:DP:GQX:MQ 0/0:116:99:22
chr1 10250 . A C 274.64 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=1.571;DP=110;DS;Dels=0.03;FS=1.342;HRun=3;HaplotypeScore=154.9171;MQ=22;MQ0=13;MQRankSum=0.056;QD=2.50;ReadPosRankSum=-0.655;SB=-86.56;VQSLOD=-23.0702;culprit=QD;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:75,31:107:99:99:22:305,0,913:0.292
chr1 10251 . C . . PASS END=10253;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:108:99:22
chr1 10254 . T . . LowGQX . GT:DP:GQX:MQ 0/0:106:0:22
chr1 10255 . A T 194.51 TruthSensitivityTranche99.90to100.00;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-1.771;DP=108;DS;Dels=0.15;FS=3.179;HRun=1;HaplotypeScore=147.3383;MQ=23;MQ0=13;MQRankSum=-0.142;QD=1.80;ReadPosRankSum=0.066;SB=-90.10;VQSLOD=-21.3642;culprit=HaplotypeScore;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:68,23:92:99:99:23:225,0,1092:0.253
chr1 10256 . A . . PASS . GT:DP:GQX:MQ 0/0:106:99:22
chr1 10257 . A C 247.88 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=2.478;DP=108;DS;Dels=0.00;FS=3.133;HRun=3;HaplotypeScore=140.1490;MQ=22;MQ0=13;MQRankSum=0.058;QD=2.30;ReadPosRankSum=0.281;SB=-65.71;VQSLOD=-20.4642;culprit=QD;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:84,24:108:99:99:22:278,0,985:0.222
chr1 10258 . C . . PASS END=10285;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:114:92:21
chr1 10286 . A . . PASS . GT:DP:GQX:MQ 0/0:117:40:23
chr1 10287 . A . . PASS END=10290;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:110:91:23
chr1 10291 . C T 258.03 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=-0.283;DP=104;DS;Dels=0.01;FS=10.488;HRun=0;HaplotypeScore=79.3731;MQ=22;MQ0=23;MQRankSum=2.521;QD=2.48;ReadPosRankSum=-2.493;SB=-81.73;VQSLOD=-12.4780;culprit=QD;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:78,22:103:99:99:22:288,0,406:0.220
chr1 10292 . A . . PASS . GT:DP:GQX:MQ 0/0:104:33:22
chr1 10293 . A . . LowGQX . GT:DP:GQX:MQ 0/0:107:9:22
chr1 10294 . C . . PASS END=10296;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:116:99:22
chr1 10297 . C T 36.25 TruthSensitivityTranche99.90to100.00;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-1.655;DP=116;DS;Dels=0.00;FS=1.882;HRun=0;HaplotypeScore=93.5449;MQ=22;MQ0=23;MQRankSum=1.292;QD=0.31;ReadPosRankSum=-1.292;SB=-6.92;VQSLOD=-15.2290;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:97,14:116:66.24:36:22:66,0,708:0.126
chr1 10298 . A . . PASS . GT:DP:GQX:MQ 0/0:115:48:22
chr1 10299 . A . . LowGQX . GT:DP:GQX:MQ 0/0:117:8:22
chr1 10300 . C . . PASS END=10303;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:121:87:22
chr1 10304 . A . . PASS END=10305;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:121:69:23
chr1 10306 . C . . PASS END=10309;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:118:84:23
chr1 10310 . A . . PASS . GT:DP:GQX:MQ 0/0:117:39:23
chr1 10311 . A . . PASS . GT:DP:GQX:MQ 0/0:119:61:23
chr1 10312 . C . . PASS END=10320;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:115:95:22
chr1 10321 . C T 30.25 TruthSensitivityTranche99.90to100.00;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-0.425;DP=121;Dels=0.00;FS=5.452;HRun=0;HaplotypeScore=112.9754;MQ=23;MQ0=21;MQRankSum=-1.333;QD=0.25;ReadPosRankSum=-1.147;SB=-0.01;VQSLOD=-17.4951;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:98,21:121:60.24:30:23:60,0,714:0.176
chr1 10322 . A . . PASS END=10326;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:119:96:23
chr1 10327 . T C 150.63 TruthSensitivityTranche99.90to100.00;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-0.619;DP=128;Dels=0.01;FS=19.248;HRun=3;HaplotypeScore=117.7001;MQ=24;MQ0=17;MQRankSum=0.017;QD=1.18;ReadPosRankSum=2.560;SB=-0.01;VQSLOD=-19.7258;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:75,48:127:99:99:24:181,0,653:0.390
chr1 10328 . A . . PASS . GT:DP:GQX:MQ 0/0:120:56:24
chr1 10329 . A . . PASS . GT:DP:GQX:MQ 0/0:127:99:24
chr1 10330 . C . 57.85 LowGQX DP=128;MQ=24;MQ0=17 GT:AD:DP:GQ:MQ:GQX 0/0:100:111:27.86:24:28
chr1 10331 . C . . PASS . GT:DP:GQX:MQ 0/0:145:99:23
chr1 10332 . C . . MaxDepth END=10333;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:155:99:23
chr1 10334 . T . . PASS . GT:DP:GQX:MQ 0/0:149:99:23
chr1 10335 . A . . MaxDepth END=10342;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:163:99:23
chr1 10343 . C . . MaxDepth END=10351;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:224:99:22
chr1 10352 . T A 121.24 TruthSensitivityTranche99.90to100.00;LowQD AC=1;AF=0.50;AN=2;BaseQRankSum=-0.425;DP=250;DS;Dels=0.04;FS=2.958;HRun=1;HaplotypeScore=297.9985;MQ=22;MQ0=35;MQRankSum=-1.385;QD=0.48;ReadPosRankSum=-4.178;SB=-67.03;VQSLOD=-95.9661;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:207,32:241:99:99:22:151,0,2079:0.134
chr1 10352 . T TA 2993.10 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=-2.585;DP=250;DS;FS=7.813;HRun=1;HaplotypeScore=1474.8577;MQ=22;MQ0=35;MQRankSum=0.249;QD=11.97;ReadPosRankSum=-0.648;SB=-466.64;VQSLOD=-2.9864;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:129,106:133:99:99:22:3032,0,535:0.451
chr1 10353 . A . . MaxDepth END=10396;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:223:99:23
chr1 10397 . C . 114.57 MaxDepth DP=250;DS;MQ=24;MQ0=42 GT:AD:DP:GQ:MQ:GQX 0/0:197:215:84.58:24:85
chr1 10398 . C . . MaxDepth END=10439;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:201:99:24
chr1 10439 . AC A 1048.36 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=1.224;DP=204;DS;FS=14.712;HRun=4;HaplotypeScore=1246.8232;MQ=25;MQ0=26;MQRankSum=-3.333;QD=5.14;ReadPosRankSum=-0.295;SB=-384.43;VQSLOD=-2.0197;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:135,62:116:99:99:25:1087,0,1719:0.315
chr1 10440 . C A . LowQD;SiteConflict;LowGQX BaseQRankSum=-1.881;DP=201;DS;Dels=0.33;FS=1.397;HRun=2;HaplotypeScore=288.5523;MQ=25;MQ0=23;MQRankSum=1.557;QD=0.35;ReadPosRankSum=0.934;SB=-24.01 GT:AD:DP:MQ .:117,17:135:25
chr1 10441 . C . . MaxDepth END=10459;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:160:99:25
chr1 10460 . C . . MaxDepth END=10461;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:150:99:27
chr1 10462 . T . . PASS . GT:DP:GQX:MQ 0/0:141:99:27
chr1 10463 . A . . LowGQX . GT:DP:GQX:MQ 0/0:128:19:28
chr1 10464 . A . . PASS END=10467;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:101:99:28
chr1 10468 . T . . PASS . GT:DP:GQX:MQ 0/0:82:99:29
chr1 10469 . C . . PASS . GT:DP:GQX:MQ 0/0:59:81:32
chr1 10470 . G . . LowGQX . GT:DP:GQX:MQ 0/0:51:5:33
chr1 10471 . C . . PASS END=10491;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:52:99:33
chr1 10492 . C T 468.93 TruthSensitivityTranche99.90to100.00 AC=1;AF=0.50;AN=2;BaseQRankSum=0.786;DP=64;Dels=0.00;FS=16.754;HRun=0;HaplotypeScore=0.9159;MQ=33;MQ0=3;MQRankSum=1.845;QD=7.33;ReadPosRankSum=-0.117;SB=-22.39;VQSLOD=-2.8812;culprit=QD;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 0/1:44,20:64:99:99:33:499,0,1263:0.313
chr1 10493 . C . . PASS END=10552;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:63:99:33
chr1 10553 . C . . PASS END=10565;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:47:99:34
chr1 10566 . A . . PASS END=10574;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:36:93:34
chr1 10575 . C . . PASS END=10585;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:30:72:33
chr1 10586 . C . . PASS END=10592;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:28:66:33
chr1 10593 . T . . PASS END=10602;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:21:42:32
chr1 10603 . G . . PASS END=10614;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:17:33:32
chr1 10615 . T . . LowGQX END=10616;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:13:18:32
chr1 10617 . C . . LowGQX . GT:DP:GQX:MQ 0/0:10:18:32
chr1 10618 . G . 39.02 LowGQX DP=11;MQ=31;MQ0=3 GT:AD:DP:GQ:MQ:GQX 0/0:6:9:9.03:31:9
chr1 10619 . C . 42.02 LowGQX DP=11;MQ=31;MQ0=3 GT:AD:DP:GQ:MQ:GQX 0/0:7:9:12.02:31:12
chr1 10620 . C . . LowGQX . GT:DP:GQX:MQ 0/0:9:15:31
chr1 10621 . G . 13.58 LowGQX DP=10;MQ=32;MQ0=3 GT:AD:DP:GQ:MQ:GQX 0/0:4:7:0.09:32:0
chr1 10622 . T G 38.24 TruthSensitivityTranche99.90to100.00;LowGQX AC=2;AF=1.00;AN=2;BaseQRankSum=0.988;DP=9;Dels=0.33;FS=0.000;HRun=1;HaplotypeScore=1.5767;MQ=27;MQ0=3;MQRankSum=1.537;QD=4.25;ReadPosRankSum=-1.537;SB=-31.26;VQSLOD=-8.0474;culprit=QD;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:3,3:6:6.02:6:27:69,6,0:0.500
chr1 10623 . T C 38.89 TruthSensitivityTranche99.90to100.00;LowGQX AC=2;AF=1.00;AN=2;DP=8;Dels=0.38;FS=0.000;HRun=0;HaplotypeScore=1.5767;MQ=25;MQ0=3;QD=4.86;SB=-0.01;VQSLOD=-8.1981;culprit=QD;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:0,5:5:6.02:6:25:70,6,0:1.000
chr1 10624 . G . 36.01 LowGQX DP=8;MQ=24;MQ0=4 GT:AD:DP:GQ:MQ:GQX 0/0:5:5:6.02:24:6
chr1 10625 . C . 36.01 LowGQX DP=10;MQ=22;MQ0=6 GT:AD:DP:GQ:MQ:GQX 0/0:7:7:6.02:22:6
chr1 10626 . A . 36.01 LowGQX DP=10;MQ=22;MQ0=6 GT:AD:DP:GQ:MQ:GQX 0/0:7:7:6.02:22:6
chr1 10627 . A . 32.98 LowGQX;LowMQ DP=9;MQ=11;MQ0=6 GT:AD:DP:GQ:MQ:GQX 0/0:6:6:3:11:3
chr1 10628 . A . 33 LowGQX;LowMQ DP=10;MQ=14;MQ0=6 GT:AD:DP:GQ:MQ:GQX 0/0:7:7:3.01:14:3
chr1 10629 . G . 36.01 LowGQX;LowMQ DP=10;MQ=14;MQ0=6 GT:AD:DP:GQ:MQ:GQX 0/0:8:8:6.02:14:6
chr1 10630 . G . 36.01 LowGQX;LowMQ DP=10;MQ=14;MQ0=6 GT:AD:DP:GQ:MQ:GQX 0/0:8:8:6.02:14:6
chr1 10631 . C . . LowGQX;LowMQ END=10632;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:10:6:15
chr1 10633 . C . 33 LowGQX;LowMQ DP=12;MQ=15;MQ0=7 GT:AD:DP:GQ:MQ:GQX 0/0:7:7:3.01:15:3
chr1 10634 . G . 36 LowGQX;LowMQ DP=13;MQ=15;MQ0=8 GT:AD:DP:GQ:MQ:GQX 0/0:9:11:6:15:6
chr1 10635 . C . 35.99 LowGQX;LowMQ DP=14;MQ=14;MQ0=9 GT:AD:DP:GQ:MQ:GQX 0/0:8:8:6:14:6
chr1 10636 . C . 39.01 LowGQX;LowMQ DP=14;MQ=14;MQ0=9 GT:AD:DP:GQ:MQ:GQX 0/0:9:11:9.01:14:9
chr1 10637 . G . 39.01 LowGQX;LowMQ DP=14;MQ=14;MQ0=9 GT:AD:DP:GQ:MQ:GQX 0/0:11:11:9.02:14:9
chr1 10638 . C . . LowGQX;LowMQ END=10641;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:15:9:15
chr1 10642 . G . 22.32 LowGQX;LowMQ DP=18;MQ=16;MQ0=11 GT:AD:DP:GQ:MQ:GQX 0/0:14:17:0.68:16:1
chr1 10643 . G . . LowGQX;LowMQ END=10646;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:19:12:15
chr1 10647 . A . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:23:6:15
chr1 10648 . G . . LowGQX;LowMQ END=10651;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:25:9:15
chr1 10652 . C . . LowGQX;LowMQ END=10659;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:25:6:14
chr1 10660 . C . . LowGQX;LowMQ END=10663;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:26:9:13
chr1 10664 . C G 5.06 TruthSensitivityTranche99.90to100.00;LowGQX;LowMQ;LowQD AC=2;AF=1.00;AN=2;BaseQRankSum=0.731;DP=25;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=4.7392;MQ=13;MQ0=19;MQRankSum=-0.731;QD=0.20;ReadPosRankSum=0.731;SB=-0.01;VQSLOD=-9.3135;culprit=MQ;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:24,1:25:3.01:3:13:33,3,0:0.040
chr1 10665 . C . 33 LowGQX;LowMQ DP=26;MQ=13;MQ0=20 GT:AD:DP:GQ:MQ:GQX 0/0:19:26:3.01:13:3
chr1 10666 . G . . LowGQX;LowMQ END=10668;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:25:6:13
chr1 10669 . C . . LowGQX;LowMQ END=10670;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:26:12:13
chr1 10671 . G . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:29:0:12
chr1 10672 . G . . LowGQX;LowMQ END=10675;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:30:6:11
chr1 10676 . A . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:35:3:11
chr1 10677 . G . . LowGQX;LowMQ END=10679;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:36:6:11
chr1 10680 . G . . LowGQX;LowMQ END=10683;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:37:9:10
chr1 10684 . A . . LowGQX;LowMQ END=10692;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:39:6:10
chr1 10693 . C . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:43:0:10
chr1 10694 . C . 36 LowGQX;LowMQ DP=45;MQ=10;MQ0=36 GT:AD:DP:GQ:MQ:GQX 0/0:33:45:6:10:6
chr1 10695 . G . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:45:6:10
chr1 10696 . C . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:50:0:9
chr1 10697 . G . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:51:12:9
chr1 10698 . C . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:51:6:9
chr1 10699 . C . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:51:12:9
chr1 10700 . G . . LowGQX;LowMQ END=10701;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:53:0:8
chr1 10702 . C . . LowGQX;LowMQ END=10704;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:53:9:8
chr1 10705 . A . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:53:3:7
chr1 10706 . G . . LowGQX;LowMQ END=10711;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:55:6:7
chr1 10712 . G . . LowGQX;LowMQ END=10716;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:59:9:8
chr1 10717 . G . . LowGQX;LowMQ END=10719;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:59:6:7
chr1 10720 . C . . LowGQX;LowMQ END=10737;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:60:9:7
chr1 10738 . G . . LowGQX;LowMQ END=10743;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:64:6:5
chr1 10744 . A . . LowGQX;LowMQ END=10745;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:65:3:4
chr1 10746 . G . . LowGQX;LowMQ END=10747 GT ./.
chr1 10748 . G . . LowGQX;LowMQ END=10760;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:47:3:4
chr1 10761 . G . . LowGQX;LowMQ END=10762;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:45:3:4
chr1 10763 . A . . LowGQX;LowMQ . GT ./.
chr1 10764 . G . . LowGQX;LowMQ END=10776;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:32:3:5
chr1 10777 . G . . LowGQX;LowMQ END=10780;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:24:3:5
chr1 10781 . C . . LowGQX;LowMQ END=10783;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:20:3:6
chr1 10784 . G . . LowGQX;LowMQ END=10787;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:14:3:7
chr1 10788 . G . . LowGQX;LowMQ END=10789;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:11:3:8
chr1 10790 . G . . LowGQX;LowMQ END=10795;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:6:3:10
chr1 10796 . G . . LowGQX;LowMQ END=10797;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:3:3:15
chr1 10798 . A . . LowGQX . GT:DP:GQX:MQ 0/0:2:3:21
chr1 10799 . G . . LowGQX END=10812;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:1:3:29
chr1 10813 . C . . LowGQX END=10820 GT ./.
chr1 10821 . T . . LowGQX;LowMQ END=12721 GT ./.
chr1 12722 . G . . LowGQX;LowMQ END=12760;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:89:3:3
chr1 12761 . C . . LowGQX;LowMQ END=12782;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:102:9:4
chr1 12783 . G A 32.97 TruthSensitivityTranche99.90to100.00;LowGQX;LowMQ;LowQD AC=2;AF=1.00;AN=2;DP=111;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=5;MQ0=96;QD=0.30;SB=-0.01;VQSLOD=-15.8461;culprit=DP;set=FilteredInAll GT:AD:DP:GQ:GQX:MQ:PL:VF 1/1:44,67:111:8.94:9:5:65,9,0:0.604
chr1 12784 . T . . LowGQX;LowMQ END=12852;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:108:9:5
chr1 12853 . A . . LowGQX;LowMQ END=12861;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:115:6:5
chr1 12862 . G . . LowGQX;LowMQ END=12899;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:105:3:5
chr1 12900 . A . . LowGQX;LowMQ END=12978 GT ./.
chr1 12979 . G . . LowGQX;LowMQ END=12980;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:107:3:2
chr1 12981 . G . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:109:9:3
chr1 12982 . C . . LowGQX;LowMQ END=12984;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:109:15:4
chr1 12985 . A . . LowGQX;LowMQ END=13014;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:110:24:5
chr1 13015 . G . . LowGQX;LowMQ END=13054;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:87:24:9
chr1 13055 . A . . LowGQX;LowMQ END=13080;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:76:21:10
chr1 13081 . A . . LowGQX;LowMQ END=13082;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:75:18:11
chr1 13083 . A . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:73:12:11
chr1 13084 . G . . LowGQX;LowMQ END=13086;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:70:3:10
chr1 13087 . A . . LowGQX;LowMQ END=13201 GT ./.
chr1 13202 . A . . LowGQX;LowMQ END=13244;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:67:3:5
chr1 13245 . A . . LowGQX;LowMQ END=13276;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:51:3:6
chr1 13277 . T . . LowGQX;LowMQ END=13290;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:39:3:6
chr1 13291 . T . . LowGQX;LowMQ END=13297;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:30:3:7
chr1 13298 . G . . LowGQX;LowMQ END=13301;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:24:3:7
chr1 13302 . C . 8.91 LowGQX;LowMQ DP=24;MQ=7;MQ0=12 GT:AD:DP:GQ:MQ:GQX 0/0:4:24:0.02:7:0
chr1 13303 . G . . LowGQX;LowMQ END=13458 GT ./.
chr1 13459 . C . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:67:3:12
chr1 13460 . A . . LowGQX;LowMQ END=13461;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:68:9:13
chr1 13462 . A . . LowGQX;LowMQ END=13465;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:66:15:13
chr1 13466 . A . . LowGQX;LowMQ END=13470;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:67:21:13
chr1 13471 . T . . LowMQ END=13484;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:67:30:13
chr1 13485 . A . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:72:27:13
chr1 13486 . G . . LowMQ END=13499;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:72:30:13
chr1 13500 . T . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:79:27:13
chr1 13501 . G . . LowMQ END=13535;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:77:30:10
chr1 13536 . A . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:80:27:10
chr1 13537 . C . . LowMQ END=13539;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:80:30:10
chr1 13540 . T . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:80:27:9
chr1 13541 . G . . LowMQ END=13559;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:79:30:7
chr1 13560 . T . . LowGQX;LowMQ END=13561;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:81:21:6
chr1 13562 . C . . LowGQX;LowMQ END=13563;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:79:15:5
chr1 13564 . G . . LowGQX;LowMQ END=13570;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:77:9:4
chr1 13571 . T . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:76:3:3
chr1 13572 . G . . LowGQX;LowMQ END=13668 GT ./.
chr1 13669 . A . . LowGQX;LowMQ END=13693;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:42:3:5
chr1 13694 . G . . LowGQX;LowMQ END=13728;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:55:3:6
chr1 13729 . T . . LowGQX;LowMQ END=13749;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:73:3:5
chr1 13750 . C . . LowGQX;LowMQ . GT:DP:GQX:MQ 0/0:80:0:5
chr1 13751 . G . . LowGQX;LowMQ END=13785;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:80:3:4
chr1 13786 . A . . LowGQX;LowMQ END=13812;BLOCKAVG_min30p3a GT:DP:GQX:MQ 0/0:103:3:3