Mercurial > repos > devteam > picard1106
view test-data/vcfFormatTest.vcf @ 90:4109d3f92a8b draft
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| author | devteam |
|---|---|
| date | Mon, 24 Feb 2014 00:38:59 -0500 |
| parents | c6b177fcac2e |
| children |
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##fileformat=VCFv4.1 ##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] read_buffer_size=null phone_home=NO_ET gatk_key=/humgen/gsa-hpprojects/GATK/data/gatk_user_keys/gsamembers_broadinstitute.org.key read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta 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=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false 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 generateShadowBCF=false logging_level=INFO log_to_file=null help=false input=[(RodBinding name=input source=/broad/hptmp/ami/tmp/CEUTrio_UG_Both_WG/CEUTrio.HiSeq.WGS.b37.listindel.unfiltered.vcf)] recal_file=(RodBinding name=recal_file source=/broad/hptmp/ami/tmp/CEUTrio_UG_Both_WG/CEUTrio.HiSeq.WGS.b37.listindel.recal) tranches_file=/broad/hptmp/ami/tmp/CEUTrio_UG_Both_WG/CEUTrio.HiSeq.WGS.b37.listindel.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=95.0 ignore_filter=null mode=INDEL filter_mismatching_base_and_quals=false" ##CombineVariants="analysis_type=CombineVariants input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta 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=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false 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 generateShadowBCF=false logging_level=INFO log_to_file=null help=false variant=[(RodBinding name=variant source=CEUTrio.HiSeq.WGS.b37.listsnp.recalibrated.filtered.vcf), (RodBinding name=variant2 source=CEUTrio.HiSeq.WGS.b37.listindel.recalibrated.filtered.vcf)] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub genotypemergeoption=UNSORTED filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=null printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=true minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_mismatching_base_and_quals=false" ##FILTER=<ID=LowQual,Description="Low quality"> ##FILTER=<ID=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -4.1718 <= x < -0.8611"> ##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -727.2136"> ##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -727.2136 <= x < -4.1718"> ##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -25.4561 <= x < 3.2489"> ##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -38672.7015"> ##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -38672.7015 <= x < -25.4561"> ##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=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##FORMAT=<ID=TP,Number=1,Type=Integer,Description="Phred score of the genotype combination and phase given that the genotypes are correct"> ##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=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> ##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=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> ##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> ##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=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> ##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> ##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=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> ##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"> ##PhaseByTransmission="analysis_type=PhaseByTransmission input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta 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=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[/broad/hptmp/ami/tmp/CEUTrio.ped] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/broad/hptmp/ami/tmp/CEUTrio_UG_Both_WG/CEUTrio.HiSeq.WGS.b37.snps_and_indels.recalibrated.filtered.vcf) DeNovoPrior=1.0E-8 FatherAlleleFirst=false out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub filter_mismatching_base_and_quals=false" ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37.list] read_buffer_size=null phone_home=NO_ET gatk_key=/humgen/gsa-hpprojects/GATK/data/gatk_user_keys/gsamembers_broadinstitute.org.key read_filter=[] intervals=[/broad/hptmp/ami/tmp/queueScatterGather/.qlog/CEUTrio.indelcall-sg/temp_020_of_300/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta 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=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=2 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 generateShadowBCF=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT pcr_error_rate=1.0E-4 noSLOD=false annotateNDA=false min_base_quality_score=17 max_deletion_fraction=0.05 cap_max_alternate_alleles_for_indels=false 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 allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.0010 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=3 dbsnp=(RodBinding name=dbsnp source=/humgen/gsa-hpprojects/GATK/bundle/current/b37/dbsnp_135.b37.vcf) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false" ##contig=<ID=1,length=249250621,assembly=b37> ##contig=<ID=2,length=243199373,assembly=b37> ##contig=<ID=3,length=198022430,assembly=b37> ##contig=<ID=4,length=191154276,assembly=b37> ##contig=<ID=5,length=180915260,assembly=b37> ##contig=<ID=6,length=171115067,assembly=b37> ##contig=<ID=7,length=159138663,assembly=b37> ##contig=<ID=8,length=146364022,assembly=b37> ##contig=<ID=9,length=141213431,assembly=b37> ##contig=<ID=10,length=135534747,assembly=b37> ##contig=<ID=11,length=135006516,assembly=b37> ##contig=<ID=12,length=133851895,assembly=b37> ##contig=<ID=13,length=115169878,assembly=b37> ##contig=<ID=14,length=107349540,assembly=b37> ##contig=<ID=15,length=102531392,assembly=b37> ##contig=<ID=16,length=90354753,assembly=b37> ##contig=<ID=17,length=81195210,assembly=b37> ##contig=<ID=18,length=78077248,assembly=b37> ##contig=<ID=19,length=59128983,assembly=b37> ##contig=<ID=20,length=63025520,assembly=b37> ##contig=<ID=21,length=48129895,assembly=b37> ##contig=<ID=22,length=51304566,assembly=b37> ##contig=<ID=X,length=155270560,assembly=b37> ##contig=<ID=Y,length=59373566,assembly=b37> ##contig=<ID=MT,length=16569,assembly=b37> ##contig=<ID=GL000207.1,length=4262,assembly=b37> ##contig=<ID=GL000226.1,length=15008,assembly=b37> ##contig=<ID=GL000229.1,length=19913,assembly=b37> ##contig=<ID=GL000231.1,length=27386,assembly=b37> ##contig=<ID=GL000210.1,length=27682,assembly=b37> ##contig=<ID=GL000239.1,length=33824,assembly=b37> ##contig=<ID=GL000235.1,length=34474,assembly=b37> ##contig=<ID=GL000201.1,length=36148,assembly=b37> ##contig=<ID=GL000247.1,length=36422,assembly=b37> ##contig=<ID=GL000245.1,length=36651,assembly=b37> ##contig=<ID=GL000197.1,length=37175,assembly=b37> ##contig=<ID=GL000203.1,length=37498,assembly=b37> ##contig=<ID=GL000246.1,length=38154,assembly=b37> ##contig=<ID=GL000249.1,length=38502,assembly=b37> ##contig=<ID=GL000196.1,length=38914,assembly=b37> ##contig=<ID=GL000248.1,length=39786,assembly=b37> ##contig=<ID=GL000244.1,length=39929,assembly=b37> ##contig=<ID=GL000238.1,length=39939,assembly=b37> ##contig=<ID=GL000202.1,length=40103,assembly=b37> ##contig=<ID=GL000234.1,length=40531,assembly=b37> ##contig=<ID=GL000232.1,length=40652,assembly=b37> ##contig=<ID=GL000206.1,length=41001,assembly=b37> ##contig=<ID=GL000240.1,length=41933,assembly=b37> ##contig=<ID=GL000236.1,length=41934,assembly=b37> ##contig=<ID=GL000241.1,length=42152,assembly=b37> ##contig=<ID=GL000243.1,length=43341,assembly=b37> ##contig=<ID=GL000242.1,length=43523,assembly=b37> ##contig=<ID=GL000230.1,length=43691,assembly=b37> ##contig=<ID=GL000237.1,length=45867,assembly=b37> ##contig=<ID=GL000233.1,length=45941,assembly=b37> ##contig=<ID=GL000204.1,length=81310,assembly=b37> ##contig=<ID=GL000198.1,length=90085,assembly=b37> ##contig=<ID=GL000208.1,length=92689,assembly=b37> ##contig=<ID=GL000191.1,length=106433,assembly=b37> ##contig=<ID=GL000227.1,length=128374,assembly=b37> ##contig=<ID=GL000228.1,length=129120,assembly=b37> ##contig=<ID=GL000214.1,length=137718,assembly=b37> ##contig=<ID=GL000221.1,length=155397,assembly=b37> ##contig=<ID=GL000209.1,length=159169,assembly=b37> ##contig=<ID=GL000218.1,length=161147,assembly=b37> ##contig=<ID=GL000220.1,length=161802,assembly=b37> ##contig=<ID=GL000213.1,length=164239,assembly=b37> ##contig=<ID=GL000211.1,length=166566,assembly=b37> ##contig=<ID=GL000199.1,length=169874,assembly=b37> ##contig=<ID=GL000217.1,length=172149,assembly=b37> ##contig=<ID=GL000216.1,length=172294,assembly=b37> ##contig=<ID=GL000215.1,length=172545,assembly=b37> ##contig=<ID=GL000205.1,length=174588,assembly=b37> ##contig=<ID=GL000219.1,length=179198,assembly=b37> ##contig=<ID=GL000224.1,length=179693,assembly=b37> ##contig=<ID=GL000223.1,length=180455,assembly=b37> ##contig=<ID=GL000195.1,length=182896,assembly=b37> ##contig=<ID=GL000212.1,length=186858,assembly=b37> ##contig=<ID=GL000222.1,length=186861,assembly=b37> ##contig=<ID=GL000200.1,length=187035,assembly=b37> ##contig=<ID=GL000193.1,length=189789,assembly=b37> ##contig=<ID=GL000194.1,length=191469,assembly=b37> ##contig=<ID=GL000225.1,length=211173,assembly=b37> ##contig=<ID=GL000192.1,length=547496,assembly=b37> ##reference=file:///humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta ##source=PhaseByTransmission #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12891 NA12892 1 8216712 rs11121115 A G 1540.26 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=0.917;DB;DP=131;Dels=0.00;FS=11.67;HaplotypeScore=3.35;MLEAC=3;MLEAF=0.500;MQ=57.74;MQ0=1;MQRankSum=0.427;QD=11.76;ReadPosRankSum=-2.190e-01;SB=-9.390e+02;VQSLOD=5.53;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0/1:23,28:51:99:681,0,668:127 0/1:16,18:34:99:338,0,244:127 0/1:24,22:46:99:560,0,323:127 1 17032814 rs2773183 T C 2828.26 VQSRTrancheSNP99.00to99.90 AC=3;AF=0.500;AN=6;BaseQRankSum=-3.879e+00;DB;DP=322;Dels=0.00;FS=2.43;HaplotypeScore=15.45;MLEAC=3;MLEAF=0.500;MQ=56.86;MQ0=0;MQRankSum=2.92;QD=8.78;ReadPosRankSum=-1.245e+00;SB=-1.943e+03;VQSLOD=-1.421e+00;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0/1:63,59:122:99:1434,0,1831:127 0/1:53,56:109:99:910,0,871:127 0/1:61,30:91:99:523,0,1257:127 1 25154033 rs55822956 GT G 743.25 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=3.32;DB;DP=214;FS=2.27;HaplotypeScore=77.33;MLEAC=3;MLEAF=0.500;MQ=55.48;MQ0=0;MQRankSum=0.114;QD=3.47;RPA=19,18;RU=T;ReadPosRankSum=0.884;SB=-3.070e+02;STR;VQSLOD=2.10;culprit=QD GT:AD:DP:GQ:PL:TP 0/1:60,12:82:67:292,0,67:18 0/1:55,7:69:42:245,0,42:18 0/1:37,21:60:18:254,0,18:18 1 36900350 rs72008966 C CA 137.53 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-3.837e+00;DB;DP=139;FS=0.00;HaplotypeScore=32.79;MLEAC=3;MLEAF=0.500;MQ=49.20;MQ0=3;MQRankSum=0.772;QD=0.990;RPA=22,23;RU=A;ReadPosRankSum=-3.220e+00;SB=-4.273e+01;STR;VQSLOD=1.87;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0/1:35,7:44:41:70,0,41:9 0/1:48,0:47:20:20,0,41:9 0/1:32,12:42:9:95,0,9:9 1 47818917 rs12749507 A G 1285.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-1.707e+00;DB;DP=252;Dels=0.00;FS=2.14;HaplotypeScore=0.666;MLEAC=1;MLEAF=0.167;MQ=59.83;MQ0=0;MQRankSum=-4.670e-01;QD=13.39;ReadPosRankSum=0.535;SB=-6.730e+02;VQSLOD=9.27;culprit=MQ GT:AD:DP:GQ:PL:TP 0|0:81,0:81:99:0,241,3171:127 0|1:53,42:96:99:1320,0,1615:127 0|0:75,0:75:99:0,217,2762:127 1 59635894 rs331648 T A 839.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-4.038e+00;DB;DP=211;Dels=0.00;FS=1.43;HaplotypeScore=1.55;MLEAC=1;MLEAF=0.167;MQ=58.68;MQ0=0;MQRankSum=-4.220e-01;QD=11.82;ReadPosRankSum=-1.800e-01;SB=-5.520e+02;VQSLOD=7.95;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:78,0:78:99:0,199,2578:127 0|0:62,0:62:99:0,169,2205:127 0|1:33,38:71:99:874,0,897:127 1 69502962 rs12724640 T C 1868.23 VQSRTrancheSNP99.00to99.90 AC=6;AF=1.00;AN=6;BaseQRankSum=-1.732e+00;DB;DP=110;Dels=0.00;FS=4.72;HaplotypeScore=1.93;MLEAC=6;MLEAF=1.00;MQ=29.46;MQ0=22;MQRankSum=1.65;QD=16.98;ReadPosRankSum=-5.640e-01;SB=-8.110e+02;VQSLOD=0.210;culprit=MQ GT:AD:DP:GQ:PL:TP 1|1:5,23:29:63:693,63,0:50 1|1:5,38:43:66:675,66,0:50 1|1:9,29:38:51:538,51,0:50 1 80481528 rs61774278 G C 1775.24 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-1.614e+00;DB;DP=168;Dels=0.00;FS=8.29;HaplotypeScore=2.05;MLEAC=3;MLEAF=0.500;MQ=54.28;MQ0=0;MQRankSum=-5.200e-02;QD=16.75;ReadPosRankSum=1.54;SB=-1.133e+03;VQSLOD=4.77;culprit=MQ GT:AD:DP:GQ:PL:TP 0|1:35,26:61:99:767,0,778:80 0|0:62,0:62:84:0,84,1046:80 1|1:0,45:45:84:1053,84,0:80 1 90146546 rs7512447 C T 8721.01 PASS AC=6;AF=1.00;AN=6;DB;DP=241;Dels=0.00;FS=0.00;HaplotypeScore=0.00;MLEAC=6;MLEAF=1.00;MQ=59.40;MQ0=0;QD=36.19;SB=-4.084e+03;VQSLOD=11.32;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:0,71:71:99:2599,196,0:127 1|1:0,86:86:99:3042,235,0:127 1|1:0,84:84:99:3080,238,0:127 1 100763317 rs6681810 G C 5583.01 PASS AC=6;AF=1.00;AN=6;DB;DP=196;Dels=0.00;FS=0.00;HaplotypeScore=3.72;MLEAC=6;MLEAF=1.00;MQ=58.52;MQ0=0;QD=28.48;SB=-2.737e+03;VQSLOD=7.92;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:1,76:77:99:2211,192,0:127 1|1:0,56:56:99:1593,141,0:127 1|1:0,62:62:99:1779,156,0:127 1 110091282 rs1279195 C T 952.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=2.65;DB;DP=101;Dels=0.00;FS=19.67;HaplotypeScore=1.92;MLEAC=2;MLEAF=0.333;MQ=56.72;MQ0=0;MQRankSum=-3.450e-01;QD=12.37;ReadPosRankSum=0.567;SB=-5.350e+02;VQSLOD=4.17;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:14,29:46:99:726,0,219:42 1|0:13,12:31:99:265,0,298:42 0|0:18,0:24:42:0,42,522:42 1 120811174 . C CA 74.77 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-1.393e+00;DP=148;FS=0.00;HaplotypeScore=20.35;MLEAC=5;MLEAF=0.833;MQ=15.79;MQ0=88;MQRankSum=-3.480e-01;QD=0.510;RPA=24,25;RU=A;ReadPosRankSum=-1.044e+00;SB=-1.531e+01;STR;VQSLOD=5.09;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:47,5:9:11:53,11,0:3 1|0:51,0:15:5:37,0,5:3 1|1:43,0:8:6:32,6,0:3 1 146610795 rs58742099 C T 2831.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.30;DB;DP=261;Dels=0.00;FS=7.03;HaplotypeScore=13.91;MLEAC=2;MLEAF=0.333;MQ=59.62;MQ0=0;MQRankSum=0.753;QD=16.27;ReadPosRankSum=-1.405e+00;SB=-1.481e+03;VQSLOD=3.42;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:39,43:82:99:1329,0,1080:127 1|0:40,52:92:99:1541,0,1241:127 0|0:87,0:87:99:0,238,3098:127 1 156248265 rs12038203 C T 643.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-3.110e-01;DB;DP=145;Dels=0.00;FS=4.57;HaplotypeScore=0.277;MLEAC=1;MLEAF=0.167;MQ=59.08;MQ0=0;MQRankSum=0.862;QD=12.86;ReadPosRankSum=0.177;SB=-3.450e+02;VQSLOD=7.50;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|0:47,0:47:99:0,123,1604:110 0|0:48,0:48:99:0,111,1433:110 0|1:25,25:50:99:678,0,694:110 1 165431906 rs7528908 G T 2381.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=6.01;DB;DP=259;Dels=0.00;FS=4.73;HaplotypeScore=0.986;MLEAC=2;MLEAF=0.333;MQ=59.75;MQ0=0;MQRankSum=0.916;QD=14.34;ReadPosRankSum=-9.070e-01;SB=-9.050e+02;VQSLOD=8.13;culprit=MQ GT:AD:DP:GQ:PL:TP 0|1:48,40:88:99:1142,0,1428:127 0|0:93,0:93:99:0,259,3166:127 1|0:38,40:78:99:1278,0,1075:127 1 175207612 rs11484568 C T 1920.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=5.64;DB;DP=216;Dels=0.00;FS=0.537;HaplotypeScore=2.25;MLEAC=2;MLEAF=0.333;MQ=58.99;MQ0=0;MQRankSum=0.383;QD=14.12;ReadPosRankSum=0.169;SB=-1.064e+03;VQSLOD=8.59;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|1:34,40:74:99:1152,0,995:127 0|0:80,0:80:99:0,208,2602:127 1|0:34,28:62:99:807,0,998:127 1 186656152 rs4422959 G A 1342.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=7.23;DB;DP=270;Dels=0.00;FS=7.29;HaplotypeScore=1.17;MLEAC=1;MLEAF=0.167;MQ=59.71;MQ0=0;MQRankSum=0.399;QD=17.21;ReadPosRankSum=-8.690e-01;SB=-6.320e+02;VQSLOD=7.67;culprit=MQ GT:AD:DP:GQ:PL:TP 0|0:99,0:99:99:0,283,3341:127 0|0:93,0:93:99:0,256,3022:127 0|1:33,45:78:99:1377,0,917:127 1 195392852 rs2119441 T G 5369.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-2.284e+00;DB;DP=241;Dels=0.00;FS=3.31;HaplotypeScore=1.87;MLEAC=4;MLEAF=0.667;MQ=58.35;MQ0=0;MQRankSum=-6.430e-01;QD=22.28;ReadPosRankSum=0.178;SB=-2.332e+03;VQSLOD=7.85;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:37,42:79:99:1233,0,1145:127 1|1:0,84:84:99:2741,211,0:127 0|1:31,47:78:99:1395,0,804:127 1 204945934 rs6657372 A G 1311.24 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-6.582e+00;DB;DP=126;Dels=0.00;FS=0.00;HaplotypeScore=2.71;MLEAC=3;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=0.480;QD=15.43;ReadPosRankSum=1.28;SB=-6.370e+02;VQSLOD=7.84;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:22,28:50:99:629,0,675:68 0|0:40,0:41:84:0,84,1057:68 1|1:0,35:35:69:727,69,0:68 1 216407409 rs3767692 A G 8820.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-8.030e-01;DB;DP=295;Dels=0.00;FS=1.35;HaplotypeScore=2.58;MLEAC=5;MLEAF=0.833;MQ=59.28;MQ0=0;MQRankSum=-3.750e-01;QD=29.90;ReadPosRankSum=-3.630e-01;SB=-4.445e+03;VQSLOD=7.05;culprit=DP GT:AD:DP:GQ:PL:TP 1|1:1,115:116:99:4251,328,0:127 1|0:39,51:90:99:1430,0,1275:127 1|1:0,89:89:99:3139,241,0:127 1 226163330 rs10915914 C G 747.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-3.123e+00;DB;DP=121;Dels=0.00;FS=0.863;HaplotypeScore=0.829;MLEAC=2;MLEAF=0.333;MQ=58.96;MQ0=0;MQRankSum=-4.780e-01;QD=9.70;ReadPosRankSum=-1.340e-01;SB=-2.780e+02;VQSLOD=8.08;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:43,1:44:99:0,117,1447:116 0|1:17,15:32:99:289,0,390:116 0|1:26,19:45:99:497,0,677:116 1 235750933 rs111686144 GA G 679.19 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=2.04;DB;DP=64;FS=7.39;HaplotypeScore=400.20;MLEAC=4;MLEAF=0.667;MQ=32.98;MQ0=0;MQRankSum=-5.900e-02;QD=10.61;ReadPosRankSum=2.44;SB=-1.575e+02;VQSLOD=-3.140e-01;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:12,0:12:6:110,0,6:6 1|1:9,9:19:31:491,31,0:6 0|1:31,0:32:99:128,0,160:6 1 243135892 rs7517403 C T 2313.25 VQSRTrancheSNP99.00to99.90 AC=4;AF=0.667;AN=6;BaseQRankSum=7.05;DB;DP=168;Dels=0.00;FS=0.00;HaplotypeScore=0.588;MLEAC=4;MLEAF=0.667;MQ=37.62;MQ0=11;MQRankSum=-5.659e+00;QD=13.77;ReadPosRankSum=-9.770e-01;SB=-9.200e+02;VQSLOD=2.25;culprit=MQ GT:AD:DP:GQ:PL:TP 1|0:31,24:55:99:501,0,891:123 1|1:0,58:58:99:1263,123,0:123 0|1:28,27:55:99:591,0,714:123 2 1143476 rs4998209 C T 1483.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-4.814e+00;DB;DP=189;Dels=0.00;FS=5.61;HaplotypeScore=0.324;MLEAC=2;MLEAF=0.333;MQ=58.36;MQ0=0;MQRankSum=1.58;QD=12.06;ReadPosRankSum=0.326;SB=-9.320e+02;VQSLOD=6.81;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|0:66,0:66:99:0,178,2264:127 0|1:33,38:71:99:844,0,1024:127 0|1:26,26:52:99:678,0,719:127 2 9240279 rs56249990 A G 3978.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=1.70;DB;DP=213;Dels=0.00;FS=7.83;HaplotypeScore=1.19;MLEAC=3;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.143;QD=27.25;ReadPosRankSum=-9.700e-02;SB=-1.991e+03;VQSLOD=9.14;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:33,42:75:99:1400,0,1031:127 0|0:67,0:67:99:0,178,2277:127 1|1:0,71:71:99:2578,199,0:127 2 18016237 rs12710649 A T 3950.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-3.700e-02;DB;DP=250;Dels=0.00;FS=2.16;HaplotypeScore=2.08;MLEAC=3;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.494;QD=15.80;ReadPosRankSum=0.705;SB=-2.142e+03;VQSLOD=8.14;culprit=FS GT:AD:DP:GQ:PL:TP 0/1:46,59:105:99:1733,0,1505:127 0/1:39,37:76:99:925,0,1164:127 0/1:24,44:68:99:1292,0,628:127 2 28790711 rs34787802 T G 731.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-4.421e+00;DB;DP=232;Dels=0.00;FS=2.40;HaplotypeScore=1.52;MLEAC=1;MLEAF=0.167;MQ=57.98;MQ0=0;MQRankSum=0.447;QD=10.30;ReadPosRankSum=-1.833e+00;SB=-4.550e+02;VQSLOD=6.89;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:81,0:81:99:0,223,2877:127 0|1:36,35:71:99:766,0,947:127 0|0:79,0:80:99:0,205,2640:127 2 36994439 rs11124542 A C 1302.26 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-7.406e+00;DB;DP=191;Dels=0.00;FS=3.34;HaplotypeScore=2.18;MLEAC=3;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=-7.250e-01;QD=6.82;ReadPosRankSum=0.302;SB=-1.006e+03;VQSLOD=7.95;culprit=QD GT:AD:DP:GQ:PL:TP 0/1:32,28:60:99:710,0,1044:127 0/1:34,25:59:99:309,0,772:127 0/1:45,27:72:99:322,0,1096:127 2 45429089 rs13418430 C A 2341.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=0.861;DB;DP=283;Dels=0.00;FS=2.85;HaplotypeScore=1.33;MLEAC=2;MLEAF=0.333;MQ=59.62;MQ0=0;MQRankSum=-9.390e-01;QD=12.52;ReadPosRankSum=-1.869e+00;SB=-1.156e+03;VQSLOD=7.15;culprit=MQ GT:AD:DP:GQ:PL:TP 1|0:60,49:109:99:1406,0,2061:127 1|0:41,37:78:99:974,0,1238:127 0|0:96,0:96:99:0,256,3312:127 2 54408283 rs55993481 T G 2128.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.96;DB;DP=222;Dels=0.00;FS=1.74;HaplotypeScore=3.96;MLEAC=2;MLEAF=0.333;MQ=59.69;MQ0=0;MQRankSum=0.670;QD=14.28;ReadPosRankSum=1.31;SB=-1.076e+03;VQSLOD=6.51;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:35,46:81:99:1392,0,921:127 1|0:35,33:68:99:775,0,878:127 0|0:73,0:73:99:0,175,2164:127 2 64848970 rs35473866 T C 655.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=0.263;DB;DP=218;Dels=0.00;FS=8.01;HaplotypeScore=2.58;MLEAC=1;MLEAF=0.167;MQ=58.36;MQ0=0;MQRankSum=-1.680e-01;QD=8.29;ReadPosRankSum=-3.070e-01;SB=-3.420e+02;VQSLOD=5.92;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:78,0:78:99:0,208,2627:127 0|0:61,0:61:99:0,135,1725:127 0|1:35,42:79:99:690,0,1042:127 2 75490647 rs112304545 T TGG 1000.21 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=0.322;DB;DP=188;FS=0.785;HaplotypeScore=58.72;MLEAC=4;MLEAF=0.667;MQ=57.19;MQ0=0;MQRankSum=-2.290e-01;QD=5.32;RPA=10,12;RU=G;ReadPosRankSum=-2.534e+00;SB=-4.650e+02;STR;VQSLOD=2.69;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:33,35:76:57:976,57,0:56 1|0:39,3:49:38:38,0,730:56 1|0:50,4:63:37:37,0,900:56 2 85513238 rs62162679 C T 742.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.16;DB;DP=137;Dels=0.00;FS=4.47;HaplotypeScore=1.39;MLEAC=2;MLEAF=0.333;MQ=57.50;MQ0=0;MQRankSum=0.479;QD=7.57;ReadPosRankSum=-2.720e-01;SB=-5.520e+02;VQSLOD=7.13;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:39,0:39:99:0,105,1267:104 0|1:23,23:47:99:430,0,551:104 0|1:31,20:51:99:351,0,633:104 2 96514373 rs10186946 C T 206.26 VQSRTrancheSNP99.00to99.90 AC=2;AF=0.333;AN=6;BaseQRankSum=4.49;DB;DP=175;Dels=0.00;FS=2.81;HaplotypeScore=2.42;MLEAC=2;MLEAF=0.333;MQ=39.07;MQ0=7;MQRankSum=-7.529e+00;QD=1.61;ReadPosRankSum=0.813;SB=-2.501e+01;VQSLOD=-8.655e-01;culprit=QD GT:AD:DP:GQ:PL:TP 1|0:35,23:58:62:62,0,484:61 1|0:22,46:70:99:183,0,387:61 0|0:46,0:47:99:0,99,1162:61 2 107234623 rs35291621 GTA G 7569 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=2.65;DB;DP=242;FS=7.84;HaplotypeScore=19.31;MLEAC=4;MLEAF=0.667;MQ=60.04;MQ0=1;MQRankSum=-1.570e-01;QD=31.28;ReadPosRankSum=1.66;SB=-3.633e+03;VQSLOD=4.30;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:46,30:76:99:1290,0,2120:127 0|1:35,66:102:99:2998,0,1435:127 1|1:0,63:63:99:3281,190,0:127 2 117966808 rs333847 C T 9037.01 PASS AC=6;AF=1.00;AN=6;DB;DP=269;Dels=0.00;FS=0.00;HaplotypeScore=3.70;MLEAC=6;MLEAF=1.00;MQ=58.21;MQ0=0;QD=33.59;SB=-4.673e+03;VQSLOD=7.05;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:0,78:78:99:2652,205,0:127 1|1:0,101:101:99:3158,247,0:127 1|1:0,89:90:99:3227,250,0:127 2 127445050 rs113647072 A G 1773.25 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-3.856e+00;DB;DP=154;Dels=0.00;FS=4.20;HaplotypeScore=2.27;MLEAC=4;MLEAF=0.667;MQ=59.16;MQ0=0;MQRankSum=0.759;QD=11.51;ReadPosRankSum=1.29;SB=-1.402e+03;VQSLOD=7.92;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|1:26,28:54:99:652,0,472:78 0|1:26,22:49:99:350,0,462:78 1|1:0,50:51:78:813,78,0:78 2 133338909 rs72548244 CT C 2103.21 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=0.444;DB;DP=212;FS=5.22;HaplotypeScore=27.63;MLEAC=5;MLEAF=0.833;MQ=59.64;MQ0=0;MQRankSum=2.43;QD=9.92;RPA=15,14;RU=T;ReadPosRankSum=2.78;SB=-1.050e+03;STR;VQSLOD=2.66;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:17,39:59:61:837,61,0:60 1|0:47,22:72:99:241,0,444:60 1|1:20,58:81:74:1076,74,0:60 2 144289763 rs7607879 C T 3308.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=1.39;DB;DP=225;Dels=0.00;FS=9.72;HaplotypeScore=1.50;MLEAC=3;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.283;QD=14.70;ReadPosRankSum=1.39;SB=-1.760e+03;VQSLOD=8.24;culprit=FS GT:AD:DP:GQ:PL:TP 0/1:41,39:81:99:1190,0,1312:127 0/1:28,36:64:99:1057,0,834:127 0/1:44,36:80:99:1061,0,1275:127 2 155726628 . T G 1351.23 VQSRTrancheSNP99.00to99.90 AC=6;AF=1.00;AN=6;BaseQRankSum=0.207;DP=193;Dels=0.00;FS=9.25;HaplotypeScore=0.522;MLEAC=6;MLEAF=1.00;MQ=16.17;MQ0=87;MQRankSum=2.40;QD=7.00;ReadPosRankSum=1.07;SB=-4.420e+02;VQSLOD=-2.787e+00;culprit=MQ GT:AD:DP:GQ:PL:TP 1|1:3,56:59:60:591,60,0:27 1|1:8,49:57:27:245,27,0:27 1|1:12,65:77:57:553,57,0:27 2 167166899 . T A 1064.78 VQSRTrancheSNP99.00to99.90 AC=5;AF=0.833;AN=6;BaseQRankSum=0.023;DP=278;Dels=0.00;FS=9.89;HaplotypeScore=0.277;MLEAC=6;MLEAF=1.00;MQ=10.47;MQ0=239;MQRankSum=1.64;QD=3.83;ReadPosRankSum=0.347;SB=-1.083e-02;VQSLOD=-6.945e+00;culprit=MQ GT:AD:DP:GQ:PL:TP 1|1:174,12:186:36:401,36,0:4 1|1:37,14:52:39:431,39,0:4 1|0:31,9:40:3:271,0,3:4 2 177175707 rs7355385 A G 2590.24 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-8.660e-01;DB;DP=206;Dels=0.00;FS=14.87;HaplotypeScore=0.311;MLEAC=3;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-9.370e-01;QD=20.40;ReadPosRankSum=-2.870e-01;SB=-8.970e+02;VQSLOD=6.82;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:33,32:65:99:856,0,1069:127 1|1:0,62:62:99:1779,150,0:127 0|0:78,1:79:99:0,193,2411:127 2 187694833 rs10191094 T C 1006.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-7.181e+00;DB;DP=236;Dels=0.00;FS=9.08;HaplotypeScore=2.27;MLEAC=1;MLEAF=0.167;MQ=59.73;MQ0=0;MQRankSum=-2.180e-01;QD=13.07;ReadPosRankSum=-8.770e-01;SB=-5.830e+02;VQSLOD=7.60;culprit=MQ GT:AD:DP:GQ:PL:TP 0|0:82,0:82:99:0,232,3021:127 0|0:77,0:77:99:0,217,2790:127 0|1:33,44:77:99:1041,0,988:127 2 198567638 rs12619333 C G 2201.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-2.800e-02;DB;DP=240;Dels=0.00;FS=4.76;HaplotypeScore=1.37;MLEAC=2;MLEAF=0.333;MQ=59.37;MQ0=1;MQRankSum=0.131;QD=13.42;ReadPosRankSum=0.123;SB=-1.051e+03;VQSLOD=8.13;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:38,45:84:99:1298,0,1249:127 1|0:45,35:80:99:942,0,1493:127 0|0:76,0:76:99:0,196,2542:127 2 209758643 rs12992166 C T 1534.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=6.18;DB;DP=163;Dels=0.00;FS=8.81;HaplotypeScore=2.36;MLEAC=2;MLEAF=0.333;MQ=58.93;MQ0=0;MQRankSum=1.99;QD=12.08;ReadPosRankSum=1.08;SB=-4.720e+02;VQSLOD=6.82;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:35,22:59:99:610,0,886:93 1|0:32,36:68:99:963,0,797:93 0|0:36,0:36:93:0,93,1058:93 2 218911764 . TA T 229.22 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=0.591;DP=218;FS=1.76;HaplotypeScore=32.57;MLEAC=3;MLEAF=0.500;MQ=57.41;MQ0=0;MQRankSum=1.79;QD=1.05;RPA=19,18;RU=A;ReadPosRankSum=0.676;SB=-1.060e+02;STR;VQSLOD=2.31;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0/1:56,5:65:99:101,0,313:70 0/1:59,18:82:99:105,0,395:70 0/1:64,4:70:71:71,0,263:70 2 228532558 rs6436725 G A 3484.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=7.16;DB;DP=263;Dels=0.00;FS=1.55;HaplotypeScore=4.97;MLEAC=3;MLEAF=0.500;MQ=58.60;MQ0=0;MQRankSum=1.14;QD=21.91;ReadPosRankSum=-4.160e-01;SB=-1.472e+03;VQSLOD=5.44;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|1:42,47:89:99:1549,0,932:127 0|0:104,0:104:99:0,247,2939:127 1|1:0,69:70:99:1935,156,0:127 2 237156689 rs13390270 G A 852.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-1.150e+00;DB;DP=205;Dels=0.00;FS=0.710;HaplotypeScore=1.73;MLEAC=1;MLEAF=0.167;MQ=59.06;MQ0=0;MQRankSum=-1.930e-01;QD=11.67;ReadPosRankSum=1.26;SB=-4.790e+02;VQSLOD=8.50;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:73,0:73:99:0,202,2606:108 0|1:39,34:73:99:887,0,1027:108 0|0:59,0:59:99:0,108,1384:108 3 1609737 rs2648459 A G 6492.01 PASS AC=6;AF=1.00;AN=6;DB;DP=187;Dels=0.00;FS=0.00;HaplotypeScore=1.18;MLEAC=6;MLEAF=1.00;MQ=59.90;MQ0=0;QD=34.72;SB=-3.251e+03;VQSLOD=11.50;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,53:53:99:1943,150,0:127 1|1:0,62:62:99:2206,172,0:127 1|1:0,72:72:99:2343,181,0:127 3 8399330 rs6770171 G A 6816.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=4.69;DB;DP=253;Dels=0.00;FS=0.637;HaplotypeScore=1.28;MLEAC=5;MLEAF=0.833;MQ=58.42;MQ0=0;MQRankSum=0.607;QD=26.94;ReadPosRankSum=-5.030e-01;SB=-3.369e+03;VQSLOD=8.01;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 1|1:0,106:106:99:3784,292,0:127 1|1:0,72:72:99:2164,169,0:127 1|0:42,33:75:99:868,0,1146:127 3 17501103 . T G 45.26 VQSRTrancheSNP99.00to99.90 AC=2;AF=0.333;AN=6;BaseQRankSum=-6.477e+00;DP=156;Dels=0.00;FS=71.75;HaplotypeScore=1.53;MLEAC=2;MLEAF=0.333;MQ=58.02;MQ0=0;MQRankSum=-1.560e-01;QD=0.430;ReadPosRankSum=-3.974e+00;SB=-1.474e-02;VQSLOD=-1.415e+01;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:43,8:51:99:0,114,1252:33 0|1:22,24:46:34:34,0,492:33 0|1:24,34:59:50:50,0,492:33 3 26960556 rs4422260 T C 878.26 VQSRTrancheSNP99.00to99.90 AC=2;AF=0.333;AN=6;BaseQRankSum=-2.140e+00;DB;DP=220;Dels=0.00;FS=1.11;HaplotypeScore=1.72;MLEAC=2;MLEAF=0.333;MQ=41.87;MQ0=3;MQRankSum=-6.679e+00;QD=5.97;ReadPosRankSum=-3.100e-02;SB=-4.600e+02;VQSLOD=0.717;culprit=MQ GT:AD:DP:GQ:PL:TP 0|0:73,0:73:99:0,208,2660:127 0|1:32,48:80:99:759,0,915:127 0|1:37,30:67:99:158,0,1092:127 3 37334187 rs112182713 G GGTT 1235.20 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=0.420;DB;DP=233;FS=10.65;HaplotypeScore=68.31;MLEAC=1;MLEAF=0.167;MQ=56.19;MQ0=0;MQRankSum=-1.868e+00;QD=17.65;RPA=1,2;RU=GTT;ReadPosRankSum=1.38;SB=-4.490e+02;STR;VQSLOD=3.14;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:83,0:83:99:0,244,4702:127 0|0:79,0:77:99:0,220,4149:127 0|1:40,23:68:99:1279,0,1696:127 3 48757773 rs61137521 A G 3103.25 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-7.940e-01;DB;DP=172;Dels=0.00;FS=0.00;HaplotypeScore=1.90;MLEAC=4;MLEAF=0.667;MQ=59.34;MQ0=0;MQRankSum=-6.930e-01;QD=18.04;ReadPosRankSum=-1.667e+00;SB=-1.874e+03;VQSLOD=7.92;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,50:51:99:1723,141,0:127 1|0:31,34:65:99:745,0,814:127 1|0:24,32:56:99:677,0,603:127 3 60283791 rs10154846 T C 669.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-3.270e+00;DB;DP=204;Dels=0.00;FS=1.59;HaplotypeScore=1.66;MLEAC=1;MLEAF=0.167;MQ=59.39;MQ0=0;MQRankSum=0.370;QD=10.14;ReadPosRankSum=1.64;SB=-2.690e+02;VQSLOD=8.95;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:63,0:63:99:0,190,2440:127 0|1:34,32:66:99:704,0,1020:127 0|0:74,0:75:99:0,190,2372:127 3 68765638 rs1504297 C G 4623.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-5.561e+00;DB;DP=225;Dels=0.00;FS=3.18;HaplotypeScore=0.843;MLEAC=4;MLEAF=0.667;MQ=59.80;MQ0=0;MQRankSum=-6.190e-01;QD=20.55;ReadPosRankSum=-1.001e+00;SB=-2.371e+03;VQSLOD=8.74;culprit=MQ GT:AD:DP:GQ:PL:TP 1|0:40,39:79:99:1220,0,1330:127 1|1:0,75:75:99:2518,205,0:127 0|1:37,34:71:99:885,0,1185:127 3 76722766 rs264537 C G 845.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=3.67;DB;DP=202;Dels=0.00;FS=0.00;HaplotypeScore=0.277;MLEAC=1;MLEAF=0.167;MQ=59.79;MQ0=0;MQRankSum=-7.950e-01;QD=13.21;ReadPosRankSum=1.05;SB=-2.910e+02;VQSLOD=8.53;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|0:70,0:70:99:0,208,2570:127 0|0:68,0:68:99:0,193,2332:127 0|1:34,30:64:99:880,0,995:127 3 86234718 rs2324883 T C 7655.01 PASS AC=6;AF=1.00;AN=6;DB;DP=234;Dels=0.00;FS=0.00;HaplotypeScore=0.649;MLEAC=6;MLEAF=1.00;MQ=59.51;MQ0=0;QD=32.71;SB=-4.142e+03;VQSLOD=11.21;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,80:80:99:2857,223,0:127 1|1:0,76:77:99:2512,196,0:127 1|1:0,77:77:99:2286,178,0:127 3 99106655 rs2623376 A G 1093.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.49;DB;DP=191;Dels=0.00;FS=2.28;HaplotypeScore=0.627;MLEAC=2;MLEAF=0.333;MQ=59.76;MQ0=0;MQRankSum=-1.141e+00;QD=9.51;ReadPosRankSum=0.079;SB=-5.610e+02;VQSLOD=8.15;culprit=QD GT:AD:DP:GQ:PL:TP 0|1:30,22:52:99:653,0,970:127 0|0:76,0:76:99:0,193,2462:127 1|0:44,19:63:99:479,0,1261:127 3 108612711 rs2399252 T A 3430.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-7.830e-01;DB;DP=239;Dels=0.00;FS=4.44;HaplotypeScore=0.659;MLEAC=3;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=-2.690e-01;QD=14.35;ReadPosRankSum=-7.010e-01;SB=-1.733e+03;VQSLOD=8.51;culprit=MQ GT:AD:DP:GQ:PL:TP 0/1:48,34:82:99:1066,0,1620:127 0/1:45,43:88:99:1370,0,1452:127 0/1:36,32:69:99:994,0,1128:127 3 118367863 rs71617664 TAGATAGATTA T 12039 PASS AC=6;AF=1.00;AN=6;BaseQRankSum=1.12;DB;DP=201;FS=9.45;HaplotypeScore=212.50;MLEAC=6;MLEAF=1.00;MQ=55.55;MQ0=1;MQRankSum=1.58;QD=59.90;ReadPosRankSum=0.721;SB=-5.599e+03;VQSLOD=-4.074e-01;culprit=QD GT:AD:DP:GQ:PL:TP 1|1:13,57:71:99:4299,164,0:127 1|1:60,4:64:99:3312,174,0:127 1|1:9,50:64:99:4428,177,0:127 3 128140891 rs73201490 C T 1315.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=5.39;DB;DP=142;Dels=0.00;FS=0.667;HaplotypeScore=3.49;MLEAC=2;MLEAF=0.333;MQ=58.69;MQ0=0;MQRankSum=1.73;QD=14.30;ReadPosRankSum=0.758;SB=-6.400e+02;VQSLOD=6.70;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|1:29,24:53:99:636,0,670:104 0|0:50,0:50:99:0,105,1188:104 1|0:12,27:39:99:718,0,250:104 3 137840974 rs2622698 C A 6792.01 PASS AC=6;AF=1.00;AN=6;DB;DP=232;Dels=0.00;FS=0.00;HaplotypeScore=2.65;MLEAC=6;MLEAF=1.00;MQ=59.04;MQ0=0;QD=29.28;SB=-3.999e+03;VQSLOD=9.77;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,79:79:99:2640,205,0:127 1|1:0,78:78:99:2229,178,0:127 1|1:0,75:75:99:1923,153,0:127 3 148344553 rs62274102 C A 3191.24 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-1.860e+00;DB;DP=232;Dels=0.00;FS=12.06;HaplotypeScore=2.37;MLEAC=3;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-5.510e-01;QD=19.58;ReadPosRankSum=2.41;SB=-1.757e+03;VQSLOD=6.29;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 1|0:46,39:85:99:985,0,1339:127 1|1:0,78:78:99:2251,175,0:127 0|0:69,0:69:99:0,153,2018:127 3 158557110 rs34445802 G A 2374.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.80;DB;DP=237;Dels=0.00;FS=1.02;HaplotypeScore=1.66;MLEAC=2;MLEAF=0.333;MQ=57.48;MQ0=0;MQRankSum=0.558;QD=14.05;ReadPosRankSum=-1.147e+00;SB=-1.505e+03;VQSLOD=7.13;culprit=MQ GT:AD:DP:GQ:PL:TP 1|0:43,56:99:99:1624,0,1344:127 1|0:33,37:70:99:789,0,916:127 0|0:68,0:68:99:0,156,2014:127 3 168108331 rs35075740 TA T 51.36 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=1.78;DB;DP=162;FS=3.97;HaplotypeScore=20.38;MLEAC=3;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=3.47;QD=0.320;RPA=18,17;RU=A;ReadPosRankSum=1.96;SB=-7.120e+00;STR;VQSLOD=2.10;culprit=QD GT:AD:DP:GQ:PL:TP 0/1:46,5:53:16:16,0,313:15 0/1:46,12:60:61:61,0,267:15 0/1:40,6:47:22:22,0,255:15 3 179020937 rs13082816 C T 1116.25 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=5.60;DB;DP=82;Dels=0.00;FS=0.00;HaplotypeScore=0.636;MLEAC=4;MLEAF=0.667;MQ=54.57;MQ0=1;MQRankSum=0.374;QD=13.61;ReadPosRankSum=-3.700e-02;SB=-2.010e+02;VQSLOD=6.09;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:13,13:26:99:388,0,178:36 1|1:0,24:24:36:442,36,0:36 0|1:13,19:32:99:328,0,179:36 3 189981901 . A G 179.25 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.167;AN=6;BaseQRankSum=2.26;DP=274;Dels=0.00;FS=73.74;HaplotypeScore=1.83;MLEAC=1;MLEAF=0.167;MQ=54.08;MQ0=6;MQRankSum=-2.651e+00;QD=1.97;ReadPosRankSum=-6.101e+00;SB=-6.400e+01;VQSLOD=-1.820e+01;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 1|0:64,27:91:99:214,0,679:51 1|0:78,10:88:0:0,21,1685:51 0|0:86,9:95:74:0,74,1891:51 3 197056886 rs7612900 G A 7880.01 PASS AC=6;AF=1.00;AN=6;DB;DP=229;Dels=0.00;FS=0.00;HaplotypeScore=0.611;MLEAC=6;MLEAF=1.00;MQ=59.18;MQ0=0;QD=34.41;SB=-3.459e+03;VQSLOD=11.81;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,75:75:99:2786,214,0:127 1|1:0,81:81:99:2598,202,0:127 1|1:0,73:73:99:2496,193,0:127 4 6333669 rs35678078 G T 2186.26 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=1.22;DB;DP=198;Dels=0.00;FS=1.75;HaplotypeScore=0.778;MLEAC=3;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=-2.560e-01;QD=11.04;ReadPosRankSum=-4.690e-01;SB=-1.621e+03;VQSLOD=9.41;culprit=QD GT:AD:DP:GQ:PL:TP 0/1:33,34:67:99:875,0,848:127 0/1:27,32:59:99:602,0,534:127 0/1:33,38:72:99:748,0,676:127 4 12652343 rs13114660 G T 610.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-3.176e+00;DB;DP=127;Dels=0.00;FS=0.00;HaplotypeScore=1.57;MLEAC=1;MLEAF=0.167;MQ=58.86;MQ0=0;MQRankSum=-4.680e-01;QD=16.06;ReadPosRankSum=1.25;SB=-3.060e+02;VQSLOD=7.84;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:43,0:43:99:0,120,1561:102 0|1:15,23:38:99:645,0,407:102 0|0:44,1:46:99:0,103,1539:102 4 21819269 rs4285068 C G 7252.01 PASS AC=6;AF=1.00;AN=6;DB;DP=216;Dels=0.00;FS=0.00;HaplotypeScore=0.651;MLEAC=6;MLEAF=1.00;MQ=55.91;MQ0=0;QD=33.57;SB=-3.284e+03;VQSLOD=8.54;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,83:83:99:2859,226,0:127 1|1:0,73:73:99:2413,193,0:127 1|1:0,59:59:99:1980,156,0:127 4 30898977 rs4386561 G A 2449.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=3.82;DB;DP=231;Dels=0.00;FS=0.00;HaplotypeScore=0.938;MLEAC=2;MLEAF=0.333;MQ=58.94;MQ0=0;MQRankSum=0.173;QD=15.70;ReadPosRankSum=1.05;SB=-1.131e+03;VQSLOD=8.36;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:33,46:79:99:1380,0,944:127 0|0:75,0:75:99:0,202,2608:127 1|0:43,34:77:99:1108,0,1335:127 4 39062189 rs2566127 T C 2641.26 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-2.019e+00;DB;DP=201;Dels=0.00;FS=1.10;HaplotypeScore=2.88;MLEAC=3;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=0.932;QD=13.14;ReadPosRankSum=-5.960e-01;SB=-1.401e+03;VQSLOD=7.97;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0/1:35,29:64:99:880,0,1168:127 0/1:37,32:70:99:796,0,1021:127 0/1:31,36:67:99:1004,0,877:127 4 48922864 rs7697262 G C 1383.23 VQSRTrancheSNP99.00to99.90 AC=6;AF=1.00;AN=6;DB;DP=100;Dels=0.00;FS=0.00;HaplotypeScore=0.00;MLEAC=6;MLEAF=1.00;MQ=20.20;MQ0=24;QD=13.83;SB=-3.860e+02;VQSLOD=-3.210e-01;culprit=MQ GT:AD:DP:GQ:PL:TP 1|1:3,38:41:57:625,57,0:32 1|1:0,28:28:33:368,33,0:32 1|1:2,29:31:39:428,39,0:32 4 57135985 rs1715504 G A 1213.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=3.55;DB;DP=173;Dels=0.00;FS=4.10;HaplotypeScore=1.63;MLEAC=2;MLEAF=0.333;MQ=58.44;MQ0=0;MQRankSum=-1.006e+00;QD=10.28;ReadPosRankSum=-9.330e-01;SB=-4.500e+02;VQSLOD=7.41;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:54,0:55:99:0,135,1546:127 0|1:30,23:54:99:563,0,608:127 0|1:35,28:64:99:689,0,562:127 4 64522064 rs4860541 A G 5942.01 PASS AC=6;AF=1.00;AN=6;DB;DP=188;Dels=0.00;FS=0.00;HaplotypeScore=0.289;MLEAC=6;MLEAF=1.00;MQ=56.20;MQ0=0;QD=31.61;SB=-3.348e+03;VQSLOD=8.54;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,68:68:99:2119,169,0:127 1|1:0,52:53:99:1661,132,0:127 1|1:0,67:67:99:2162,172,0:127 4 71449060 rs60358213 G A 2269.26 VQSRTrancheSNP99.00to99.90 AC=2;AF=0.333;AN=6;BaseQRankSum=5.70;DB;DP=227;Dels=0.00;FS=13.05;HaplotypeScore=20.14;MLEAC=2;MLEAF=0.333;MQ=55.35;MQ0=0;MQRankSum=0.477;QD=13.19;ReadPosRankSum=2.30;SB=-8.910e+02;VQSLOD=1.89;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:60,40:100:99:1221,0,1476:127 1|0:37,35:72:99:1087,0,987:127 0|0:53,1:54:99:0,157,2026:127 4 82427976 rs6841516 G A 561.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-1.022e+00;DB;DP=166;Dels=0.00;FS=0.00;HaplotypeScore=1.47;MLEAC=1;MLEAF=0.167;MQ=59.56;MQ0=0;MQRankSum=-1.555e+00;QD=11.00;ReadPosRankSum=0.016;SB=-3.880e+02;VQSLOD=8.10;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:51,0:51:99:0,132,1705:127 0|1:22,29:51:99:596,0,483:127 0|0:64,0:64:99:0,135,1755:127 4 92648168 rs61329801 A ATTTG 7717 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=0.947;DB;DP=186;FS=8.29;HaplotypeScore=7.88;MLEAC=4;MLEAF=0.667;MQ=56.58;MQ0=0;MQRankSum=-1.740e-01;QD=41.49;ReadPosRankSum=-4.440e-01;SB=-3.591e+03;VQSLOD=3.52;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:45,35:80:99:2213,0,2213:127 1|1:3,59:62:99:4128,181,0:127 0|1:22,22:44:99:1376,0,1181:127 4 103859292 rs7676943 C G 7573.01 PASS AC=6;AF=1.00;AN=6;DB;DP=235;Dels=0.00;FS=0.00;HaplotypeScore=0.00;MLEAC=6;MLEAF=1.00;MQ=58.63;MQ0=0;QD=32.23;SB=-3.953e+03;VQSLOD=10.39;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:1,95:96:99:3289,256,0:127 1|1:0,73:73:99:2137,166,0:127 1|1:0,66:66:99:2147,166,0:127 4 114869733 rs11381039 A AT 2798.22 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=0.957;DB;DP=267;FS=4.37;HaplotypeScore=26.36;MLEAC=3;MLEAF=0.500;MQ=59.97;MQ0=0;MQRankSum=0.673;QD=10.48;RPA=8,9;RU=T;ReadPosRankSum=-1.351e+00;SB=-1.173e+03;STR;VQSLOD=5.55;culprit=QD GT:AD:DP:GQ:PL:TP 0/1:47,41:89:99:994,0,1219:127 0/1:50,41:92:99:1063,0,1043:127 0/1:50,34:86:99:789,0,1153:127 4 122900130 rs4833786 C T 2361.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-3.900e-01;DB;DP=244;Dels=0.00;FS=0.495;HaplotypeScore=0.543;MLEAC=2;MLEAF=0.333;MQ=59.91;MQ0=0;MQRankSum=-6.280e-01;QD=15.23;ReadPosRankSum=1.22;SB=-1.282e+03;VQSLOD=8.81;culprit=MQ GT:AD:DP:GQ:PL:TP 0|0:89,0:89:99:0,250,3286:127 0|1:42,44:86:99:1257,0,1325:127 0|1:32,37:69:99:1143,0,941:127 4 132671861 rs6856716 C G 2622.26 VQSRTrancheSNP99.90to100.00 AC=2;AF=0.333;AN=6;BaseQRankSum=3.14;DB;DP=617;DS;Dels=0.00;FS=5.81;HaplotypeScore=34.41;MLEAC=2;MLEAF=0.333;MQ=24.78;MQ0=42;MQRankSum=3.29;QD=5.89;ReadPosRankSum=-7.360e-01;SB=-1.412e+03;VQSLOD=-7.735e+01;culprit=DP GT:AD:DP:GQ:PL:TP 0|1:125,98:223:99:1761,0,1486:127 0|0:171,0:172:99:0,300,2641:127 1|0:152,70:222:99:900,0,2086:127 4 141514835 rs55984232 C T 1645.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=7.14;DB;DP=191;Dels=0.00;FS=2.76;HaplotypeScore=1.07;MLEAC=2;MLEAF=0.333;MQ=59.26;MQ0=0;MQRankSum=0.726;QD=13.06;ReadPosRankSum=-7.890e-01;SB=-8.550e+02;VQSLOD=8.94;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:32,28:60:99:913,0,820:127 0|0:65,0:65:99:0,156,1886:127 1|0:34,32:66:99:771,0,750:127 4 152029268 . CT C 358.22 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=2.69;DP=199;FS=13.72;HaplotypeScore=32.57;MLEAC=2;MLEAF=0.333;MQ=55.17;MQ0=0;MQRankSum=-9.150e-01;QD=2.42;RPA=17,16;RU=T;ReadPosRankSum=0.548;SB=-1.419e+02;STR;VQSLOD=0.393;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:50,15:75:99:301,0,225:38 1|0:56,11:72:99:105,0,209:38 0|0:46,2:51:38:0,38,284:38 4 161180100 rs167176 G C 2497.26 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=6.81;DB;DP=191;Dels=0.00;FS=5.37;HaplotypeScore=0.781;MLEAC=3;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=-5.840e-01;QD=13.07;ReadPosRankSum=0.756;SB=-1.206e+03;VQSLOD=8.00;culprit=MQ GT:AD:DP:GQ:PL:TP 0/1:32,36:68:99:1100,0,895:127 0/1:41,35:76:99:987,0,1028:127 0/1:29,17:47:99:449,0,820:127 4 169085855 rs2251558 A G 1161.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=0.721;DB;DP=244;Dels=0.00;FS=5.25;HaplotypeScore=0.489;MLEAC=1;MLEAF=0.167;MQ=59.91;MQ0=0;MQRankSum=1.57;QD=13.99;ReadPosRankSum=0.454;SB=-5.590e+02;VQSLOD=7.42;culprit=MQ GT:AD:DP:GQ:PL:TP 0|0:77,0:77:99:0,226,2915:127 0|1:43,40:83:99:1196,0,1294:127 0|0:84,0:84:99:0,232,2950:127 4 177855678 rs1545090 A G 7065.01 PASS AC=6;AF=1.00;AN=6;DB;DP=229;Dels=0.00;FS=0.00;HaplotypeScore=1.17;MLEAC=6;MLEAF=1.00;MQ=59.50;MQ0=0;QD=30.85;SB=-3.799e+03;VQSLOD=11.01;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,84:84:99:2701,235,0:127 1|1:0,79:80:99:2401,211,0:127 1|1:0,65:65:99:1963,165,0:127 4 184811263 rs2871379 A G 6376.01 PASS AC=6;AF=1.00;AN=6;DB;DP=211;Dels=0.00;FS=0.00;HaplotypeScore=0.508;MLEAC=6;MLEAF=1.00;MQ=58.38;MQ0=0;QD=30.22;SB=-3.472e+03;VQSLOD=10.49;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,78:78:99:2539,199,0:127 1|1:0,67:67:99:2072,165,0:127 1|1:0,66:66:99:1765,135,0:127 4 190538070 rs62323772 G A 106.69 VQSRTrancheSNP99.00to99.90 AC=3;AF=0.500;AN=6;BaseQRankSum=0.099;DB;DP=19;Dels=0.00;FS=0.00;HaplotypeScore=4.36;MLEAC=3;MLEAF=0.500;MQ=33.71;MQ0=0;MQRankSum=0.591;QD=5.93;ReadPosRankSum=-3.940e-01;SB=-7.601e+01;VQSLOD=-1.392e+00;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|1:4,9:13:69:69,0,92:3 0|0:1,0:1:3:0,3,33:3 1|1:0,4:5:6:77,6,0:3 5 3276081 rs4866540 G A 3653.01 VQSRTrancheSNP99.00to99.90 AC=4;AF=0.667;AN=6;BaseQRankSum=5.00;DB;DP=176;Dels=0.00;FS=2.78;HaplotypeScore=19.00;MLEAC=4;MLEAF=0.667;MQ=57.74;MQ0=0;MQRankSum=-5.690e-01;QD=20.76;ReadPosRankSum=1.31;SB=-6.610e+02;VQSLOD=3.18;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:1,71:72:99:2337,175,0:127 1|0:26,25:51:99:719,0,601:127 1|0:26,27:53:99:597,0,662:127 5 10958957 rs852590 T C 8430.01 PASS AC=6;AF=1.00;AN=6;DB;DP=243;Dels=0.00;FS=0.00;HaplotypeScore=1.83;MLEAC=6;MLEAF=1.00;MQ=59.31;MQ0=0;QD=34.69;SB=-4.118e+03;VQSLOD=10.87;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:1,96:97:99:3594,277,0:127 1|1:1,73:74:99:2318,181,0:127 1|1:0,72:72:99:2518,196,0:127 5 20435939 rs12697584 A C 2286.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-5.396e+00;DB;DP=246;Dels=0.00;FS=4.68;HaplotypeScore=0.874;MLEAC=2;MLEAF=0.333;MQ=59.74;MQ0=0;MQRankSum=-8.500e-01;QD=14.20;ReadPosRankSum=0.391;SB=-1.305e+03;VQSLOD=8.13;culprit=MQ GT:AD:DP:GQ:PL:TP 0|0:85,0:85:99:0,241,3183:127 0|1:41,37:78:99:1062,0,1304:127 0|1:39,44:83:99:1263,0,1222:127 5 29069162 rs658439 G A 499.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=1.98;DB;DP=199;Dels=0.00;FS=11.20;HaplotypeScore=1.60;MLEAC=1;MLEAF=0.167;MQ=52.70;MQ0=0;MQRankSum=-6.080e-01;QD=9.42;ReadPosRankSum=-1.103e+00;SB=-2.310e+02;VQSLOD=4.02;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:86,0:86:99:0,211,2509:110 0|0:60,0:60:99:0,111,1240:110 0|1:30,23:53:99:534,0,523:110 5 36740339 rs36676 T G 6995.01 PASS AC=6;AF=1.00;AN=6;DB;DP=230;Dels=0.00;FS=0.00;HaplotypeScore=2.08;MLEAC=6;MLEAF=1.00;MQ=59.46;MQ0=0;QD=30.41;SB=-3.034e+03;VQSLOD=10.92;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,75:75:99:2261,195,0:127 1|1:0,83:83:99:2579,217,0:127 1|1:0,71:72:99:2155,181,0:127 5 49438828 rs137880658 G A 424.24 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.167;AN=6;BaseQRankSum=-4.376e+00;DB;DP=748;DS;Dels=0.00;FS=7.18;HaplotypeScore=20.66;MLEAC=1;MLEAF=0.167;MQ=19.63;MQ0=158;MQRankSum=3.82;QD=1.70;ReadPosRankSum=1.19;SB=-2.220e+02;VQSLOD=-9.822e+01;culprit=DP GT:AD:DP:GQ:PL:TP 0|0:249,0:249:99:0,555,4848:127 0|1:204,46:250:99:459,0,2894:127 0|0:249,0:249:99:0,480,4326:127 5 58243302 rs457566 A C 6237.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-1.663e+00;DB;DP=233;Dels=0.00;FS=3.43;HaplotypeScore=0.886;MLEAC=5;MLEAF=0.833;MQ=59.70;MQ0=0;MQRankSum=-2.320e-01;QD=26.77;ReadPosRankSum=0.957;SB=-2.566e+03;VQSLOD=9.35;culprit=MQ GT:AD:DP:GQ:PL:TP 1|1:0,87:87:99:2923,229,0:127 1|0:36,50:86:99:1429,0,1006:127 1|1:0,60:60:99:1885,147,0:127 5 70856663 rs157045 T C 2040.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-7.809e+00;DB;DP=234;Dels=0.00;FS=1.82;HaplotypeScore=1.05;MLEAC=2;MLEAF=0.333;MQ=58.65;MQ0=0;MQRankSum=0.989;QD=13.16;ReadPosRankSum=0.719;SB=-8.820e+02;VQSLOD=7.35;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:44,41:85:99:1087,0,1448:127 1|0:28,42:70:99:992,0,789:127 0|0:79,0:79:99:0,181,2342:127 5 80900719 rs2917540 G T 4938.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=3.26;DB;DP=240;Dels=0.00;FS=0.489;HaplotypeScore=0.596;MLEAC=4;MLEAF=0.667;MQ=59.63;MQ0=0;MQRankSum=-2.115e+00;QD=20.58;ReadPosRankSum=0.288;SB=-2.548e+03;VQSLOD=8.44;culprit=MQ GT:AD:DP:GQ:PL:TP 0|1:52,40:92:99:1207,0,1768:127 0|1:37,33:70:99:960,0,1205:127 1|1:0,78:78:99:2771,211,0:127 5 93119893 rs6879620 G A 4262.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=4.93;DB;DP=239;Dels=0.00;FS=1.05;HaplotypeScore=2.16;MLEAC=4;MLEAF=0.667;MQ=59.81;MQ0=0;MQRankSum=0.891;QD=17.83;ReadPosRankSum=-2.670e+00;SB=-2.596e+03;VQSLOD=7.07;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 0|1:49,42:91:99:1098,0,1410:127 0|1:36,38:74:99:890,0,1008:127 1|1:0,74:74:99:2274,178,0:127 5 102962771 rs6866105 A G 5087.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-2.665e+00;DB;DP=200;Dels=0.00;FS=8.08;HaplotypeScore=2.28;MLEAC=5;MLEAF=0.833;MQ=58.71;MQ0=0;MQRankSum=-5.030e-01;QD=25.44;ReadPosRankSum=-4.820e-01;SB=-2.172e+03;VQSLOD=7.22;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,75:75:99:2373,184,0:127 1|1:0,59:59:99:1776,141,0:127 1|0:31,35:66:99:938,0,803:127 5 112750674 rs9716322 A C 598.24 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.167;AN=6;BaseQRankSum=-2.930e-01;DB;DP=199;Dels=0.00;FS=2.95;HaplotypeScore=0.333;MLEAC=1;MLEAF=0.167;MQ=45.61;MQ0=2;MQRankSum=-2.398e+00;QD=12.21;ReadPosRankSum=1.16;SB=-8.101e+01;VQSLOD=2.77;culprit=MQ GT:AD:DP:GQ:PL:TP 0|0:81,0:81:99:0,196,2534:127 0|1:23,26:49:99:633,0,479:127 0|0:68,1:69:99:0,174,2191:127 5 121302662 . G T 143.72 VQSRTrancheSNP99.90to100.00 AC=3;AF=0.500;AN=6;BaseQRankSum=1.41;DP=150;Dels=0.020;FS=161.48;HaplotypeScore=2.86;MLEAC=3;MLEAF=0.500;MQ=35.76;MQ0=1;MQRankSum=0.422;QD=0.960;ReadPosRankSum=-5.675e+00;SB=-1.466e+00;VQSLOD=-7.724e+01;culprit=FS GT:AD:DP:GQ:PL:TP 0/1:32,21:53:99:120,0,251:5 0/1:35,12:47:57:57,0,271:5 0/1:35,12:47:4:4,0,259:5 5 132377304 rs72801439 A T 858.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-1.113e+00;DB;DP=219;Dels=0.00;FS=10.63;HaplotypeScore=0.664;MLEAC=1;MLEAF=0.167;MQ=59.41;MQ0=0;MQRankSum=-8.810e-01;QD=11.29;ReadPosRankSum=0.435;SB=-3.050e+02;VQSLOD=7.68;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:67,0:67:99:0,163,2149:127 0|1:43,33:76:99:893,0,1280:127 0|0:76,0:76:99:0,199,2553:127 5 144321895 rs35068704 A T 1535.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=6.05;DB;DP=203;Dels=0.00;FS=13.29;HaplotypeScore=0.507;MLEAC=2;MLEAF=0.333;MQ=57.36;MQ0=0;MQRankSum=2.19;QD=11.37;ReadPosRankSum=-1.361e+00;SB=-7.640e+02;VQSLOD=5.72;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:34,25:59:99:595,0,976:127 0|0:68,0:68:99:0,190,2435:127 1|0:39,37:76:99:979,0,1274:127 5 154441640 rs467330 A C 1133.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-1.127e+00;DB;DP=235;Dels=0.00;FS=2.10;HaplotypeScore=1.19;MLEAC=1;MLEAF=0.167;MQ=59.65;MQ0=0;MQRankSum=0.766;QD=12.59;ReadPosRankSum=-5.350e-01;SB=-6.500e+02;VQSLOD=9.83;culprit=MQ GT:AD:DP:GQ:PL:TP 0|0:61,0:61:99:0,172,2172:127 0|1:45,45:90:99:1168,0,1368:127 0|0:82,1:84:99:0,226,2825:127 5 164600452 rs7711548 C A 588.32 VQSRTrancheSNP99.00to99.90 AC=6;AF=1.00;AN=6;BaseQRankSum=-3.291e+00;DB;DP=192;Dels=0.020;FS=2.32;HaplotypeScore=32.67;MLEAC=6;MLEAF=1.00;MQ=57.55;MQ0=0;MQRankSum=1.54;QD=3.06;ReadPosRankSum=-1.533e+00;SB=-2.085e+03;VQSLOD=-1.433e+00;culprit=QD GT:AD:DP:GQ:PL:TP 1|1:15,52:69:18:155,18,0:15 1|1:11,55:66:36:296,36,0:15 1|1:18,36:54:15:175,15,0:15 5 174249229 rs11739079 C G 1613.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-4.540e+00;DB;DP=190;Dels=0.00;FS=6.48;HaplotypeScore=2.04;MLEAC=2;MLEAF=0.333;MQ=59.51;MQ0=0;MQRankSum=-8.980e-01;QD=11.86;ReadPosRankSum=0.601;SB=-8.320e+02;VQSLOD=7.78;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:32,43:75:99:1069,0,928:123 0|0:54,0:54:99:0,123,1554:123 1|0:33,27:61:99:583,0,883:123 6 1620147 rs2569882 T C 252.30 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-8.620e-01;DB;DP=38;Dels=0.00;FS=8.02;HaplotypeScore=0.222;MLEAC=5;MLEAF=0.833;MQ=57.65;MQ0=0;MQRankSum=-9.180e-01;QD=9.34;ReadPosRankSum=0.584;SB=-4.005e+01;VQSLOD=4.33;culprit=DP GT:AD:DP:GQ:PL:TP 1|1:0,17:17:21:254,21,0:4 1|0:3,8:11:2:0,3,40:4 1|1:0,10:10:3:39,3,0:4 6 9408051 rs11751621 C G 5140.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-2.350e+00;DB;DP=241;Dels=0.00;FS=0.00;HaplotypeScore=0.664;MLEAC=4;MLEAF=0.667;MQ=59.81;MQ0=0;MQRankSum=-2.050e-01;QD=21.33;ReadPosRankSum=-3.300e-02;SB=-2.552e+03;VQSLOD=8.99;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:42,40:82:99:1156,0,1352:127 0|1:36,45:81:99:1253,0,1134:127 1|1:0,78:78:99:2731,214,0:127 6 18687376 rs9383429 A T 1162.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-2.746e+00;DB;DP=232;Dels=0.00;FS=0.638;HaplotypeScore=0.277;MLEAC=1;MLEAF=0.167;MQ=59.42;MQ0=0;MQRankSum=-7.330e-01;QD=15.71;ReadPosRankSum=-1.460e-01;SB=-6.490e+02;VQSLOD=9.43;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|0:82,0:82:99:0,241,3181:127 0|0:76,0:76:99:0,217,2832:127 0|1:33,41:74:99:1197,0,1008:127 6 26687649 . G C 1654.26 VQSRTrancheSNP99.00to99.90 AC=2;AF=0.333;AN=6;BaseQRankSum=9.72;DP=410;Dels=0.00;FS=5.97;HaplotypeScore=5.08;MLEAC=2;MLEAF=0.333;MQ=28.19;MQ0=32;MQRankSum=0.048;QD=6.17;ReadPosRankSum=0.408;SB=-5.110e+02;VQSLOD=-8.735e+00;culprit=DP GT:AD:DP:GQ:PL:TP 0|1:117,49:166:99:1013,0,2495:127 0|0:141,1:142:99:0,244,2576:127 1|0:70,32:102:99:680,0,1048:127 6 31390139 rs72548006 T TA 2159.22 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=0.491;DB;DP=257;FS=2.38;HaplotypeScore=26.89;MLEAC=2;MLEAF=0.333;MQ=59.99;MQ0=0;MQRankSum=1.59;QD=12.85;RPA=5,6;RU=A;ReadPosRankSum=1.85;SB=-9.710e+02;STR;VQSLOD=5.53;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|1:51,37:89:99:1076,0,1364:127 0|0:89,0:89:99:0,256,3112:127 1|0:41,38:79:99:1131,0,1103:127 6 35346891 . C T 483.26 VQSRTrancheSNP99.90to100.00 AC=3;AF=0.500;AN=6;BaseQRankSum=-6.402e+00;DP=205;Dels=0.020;FS=214.15;HaplotypeScore=4.51;MLEAC=3;MLEAF=0.500;MQ=51.07;MQ0=1;MQRankSum=-2.038e+00;QD=2.36;ReadPosRankSum=-2.250e+00;SB=-1.065e-02;VQSLOD=-1.170e+02;culprit=FS GT:AD:DP:GQ:PL:TP 0/1:48,31:79:99:257,0,635:80 0/1:40,22:62:99:185,0,308:80 0/1:44,16:60:80:80,0,534:80 6 45421630 rs1343799 C T 5422.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=3.42;DB;DP=240;Dels=0.00;FS=10.69;HaplotypeScore=0.798;MLEAC=4;MLEAF=0.667;MQ=59.46;MQ0=0;MQRankSum=1.09;QD=22.59;ReadPosRankSum=1.25;SB=-2.647e+03;VQSLOD=7.70;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:29,43:72:99:1445,0,843:127 0|1:43,37:80:99:1121,0,1302:127 1|1:0,88:88:99:2856,220,0:127 6 55412503 rs12201934 T C 882.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-1.280e+00;DB;DP=182;Dels=0.00;FS=0.744;HaplotypeScore=0.333;MLEAC=1;MLEAF=0.167;MQ=59.64;MQ0=0;MQRankSum=-7.650e-01;QD=13.57;ReadPosRankSum=0.147;SB=-4.590e+02;VQSLOD=9.38;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|0:61,0:61:99:0,181,2371:127 0|1:35,30:65:99:917,0,1046:127 0|0:56,0:56:99:0,150,1969:127 6 63303894 rs34270846 T TC 7366 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=1.31;DB;DP=202;FS=2.81;HaplotypeScore=88.29;MLEAC=5;MLEAF=0.833;MQ=61.10;MQ0=0;MQRankSum=-3.900e-01;QD=36.47;ReadPosRankSum=-3.150e-01;SB=-2.762e+03;VQSLOD=3.86;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,89:89:99:3885,265,0:127 1|0:29,25:54:99:999,0,1050:127 1|1:0,57:59:99:2482,169,0:127 6 71018445 rs1321063 C A 518.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=2.67;DB;DP=185;Dels=0.00;FS=1.62;HaplotypeScore=0.692;MLEAC=1;MLEAF=0.167;MQ=58.93;MQ0=0;MQRankSum=0.355;QD=8.78;ReadPosRankSum=1.31;SB=-4.020e+02;VQSLOD=7.75;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:67,0:67:99:0,184,2404:127 0|0:59,0:59:99:0,160,2065:127 0|1:29,30:59:99:553,0,809:127 6 79887872 rs6454101 C T 2130.26 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-3.355e+00;DB;DP=204;Dels=0.00;FS=11.82;HaplotypeScore=2.38;MLEAC=3;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=1.01;QD=10.44;ReadPosRankSum=-7.690e-01;SB=-1.370e+03;VQSLOD=7.52;culprit=MQ GT:AD:DP:GQ:PL:TP 0/1:31,31:62:99:806,0,990:127 0/1:42,31:73:99:606,0,921:127 0/1:29,40:69:99:757,0,749:127 6 89947117 rs9942462 A G 5019.01 PASS AC=6;AF=1.00;AN=6;BaseQRankSum=1.65;DB;DP=181;Dels=0.00;FS=0.00;HaplotypeScore=3.32;MLEAC=6;MLEAF=1.00;MQ=53.30;MQ0=0;MQRankSum=0.428;QD=27.73;ReadPosRankSum=1.09;SB=-3.151e+03;VQSLOD=5.68;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:0,59:60:99:1715,138,0:92 1|1:1,55:56:93:1401,93,0:92 1|1:0,65:65:99:1903,153,0:92 6 100462085 rs113348222 G GT 5284 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-4.600e-02;DB;DP=285;FS=7.48;HaplotypeScore=252.09;MLEAC=5;MLEAF=0.833;MQ=60.07;MQ0=0;MQRankSum=1.24;QD=18.54;RPA=10,11;RU=T;ReadPosRankSum=-2.539e+00;SB=-2.505e+03;STR;VQSLOD=2.21;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 1|1:8,79:94:99:2218,200,0:127 1|0:54,37:97:99:818,0,914:127 1|1:10,83:94:99:2248,221,0:127 6 110345430 rs56272355 T C 882.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-7.241e+00;DB;DP=230;Dels=0.00;FS=2.16;HaplotypeScore=1.76;MLEAC=1;MLEAF=0.167;MQ=59.70;MQ0=0;MQRankSum=-2.000e-01;QD=11.46;ReadPosRankSum=-4.800e-01;SB=-5.580e+02;VQSLOD=8.98;culprit=MQ GT:AD:DP:GQ:PL:TP 0|0:77,0:77:99:0,220,2860:127 0|0:75,0:76:99:0,184,2321:127 0|1:35,42:77:99:917,0,926:127 6 120734422 rs62424426 T C 1091.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-3.268e+00;DB;DP=208;Dels=0.00;FS=4.35;HaplotypeScore=0.703;MLEAC=1;MLEAF=0.167;MQ=59.71;MQ0=0;MQRankSum=-1.880e-01;QD=14.36;ReadPosRankSum=-1.490e-01;SB=-5.560e+02;VQSLOD=8.65;culprit=MQ GT:AD:DP:GQ:PL:TP 0|0:70,1:71:99:0,205,2692:127 0|0:61,0:61:99:0,175,2298:127 0|1:39,37:76:99:1126,0,1140:127 6 131725921 . G A 64.24 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.167;AN=6;BaseQRankSum=3.65;DP=182;Dels=0.00;FS=3.54;HaplotypeScore=2.24;MLEAC=1;MLEAF=0.167;MQ=50.85;MQ0=1;MQRankSum=-6.039e+00;QD=1.31;ReadPosRankSum=-1.757e+00;SB=-4.901e+01;VQSLOD=-6.667e-01;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:59,0:60:99:0,168,1897:98 0|1:33,16:49:99:99,0,790:98 0|0:73,0:73:99:0,156,1824:98 6 143691852 rs17792267 C T 3641.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-1.465e+00;DB;DP=203;Dels=0.00;FS=2.41;HaplotypeScore=0.322;MLEAC=3;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=1.20;QD=27.17;ReadPosRankSum=-1.140e+00;SB=-1.772e+03;VQSLOD=8.87;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:29,33:62:99:1131,0,803:127 1|1:0,72:72:99:2510,196,0:127 0|0:69,0:69:99:0,190,2480:127 6 154006585 rs7752561 G A 919.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-2.323e+00;DB;DP=223;Dels=0.00;FS=0.00;HaplotypeScore=0.825;MLEAC=1;MLEAF=0.167;MQ=59.35;MQ0=0;MQRankSum=-7.490e-01;QD=10.45;ReadPosRankSum=-1.550e-01;SB=-5.260e+02;VQSLOD=8.84;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:70,0:70:99:0,202,2601:127 0|1:51,37:88:99:954,0,1475:127 0|0:65,0:65:99:0,175,2269:127 6 162459664 rs2849564 C T 1819.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=8.40;DB;DP=201;Dels=0.00;FS=3.30;HaplotypeScore=2.56;MLEAC=2;MLEAF=0.333;MQ=59.38;MQ0=0;MQRankSum=1.79;QD=12.90;ReadPosRankSum=-1.045e+00;SB=-1.068e+03;VQSLOD=8.12;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:28,40:68:99:1007,0,793:120 1|0:38,35:73:99:851,0,831:120 0|0:60,0:60:99:0,120,1421:120 6 169196022 . T TG 229.23 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=0.887;DP=84;FS=7.13;HaplotypeScore=6.43;MLEAC=2;MLEAF=0.333;MQ=39.46;MQ0=16;MQRankSum=2.28;QD=3.82;RPA=6,7;RU=G;ReadPosRankSum=-9.830e-01;SB=-2.849e+01;STR;VQSLOD=1.35;culprit=QD GT:AD:DP:GQ:PL:TP 1|0:19,10:15:78:78,0,88:27 1|0:17,13:21:99:199,0,172:27 0|0:24,0:15:27:0,27,308:27 7 4683258 rs62450857 G A 1127.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-9.910e-01;DB;DP=191;Dels=0.00;FS=3.24;HaplotypeScore=0.277;MLEAC=1;MLEAF=0.167;MQ=57.16;MQ0=0;MQRankSum=1.30;QD=14.09;ReadPosRankSum=0.469;SB=-4.730e+02;VQSLOD=6.62;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|0:66,0:66:99:0,196,2495:120 0|1:38,42:80:99:1162,0,1016:120 0|0:45,0:45:99:0,120,1531:120 7 12502849 rs848025 C G 4109.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-8.809e+00;DB;DP=220;Dels=0.00;FS=1.14;HaplotypeScore=1.80;MLEAC=4;MLEAF=0.667;MQ=59.56;MQ0=0;MQRankSum=0.625;QD=18.68;ReadPosRankSum=-1.900e-02;SB=-1.989e+03;VQSLOD=8.71;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:47,45:92:99:1216,0,1501:127 1|1:0,71:71:99:2145,184,0:127 0|1:27,30:57:99:748,0,743:127 7 20767781 rs150977587 TA T 2754.21 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=6.30;DB;DP=259;FS=0.00;HaplotypeScore=122.50;MLEAC=4;MLEAF=0.667;MQ=59.41;MQ0=1;MQRankSum=-6.400e-01;QD=10.63;RPA=13,12;RU=A;ReadPosRankSum=0.189;SB=-1.344e+03;STR;VQSLOD=3.30;culprit=QD GT:AD:DP:GQ:PL:TP 1|0:59,45:107:99:923,0,795:116 1|1:15,54:72:99:1313,116,0:116 0|1:44,31:79:99:569,0,617:116 7 29544610 rs6462145 A T 4020.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=0.326;DB;DP=189;Dels=0.00;FS=5.39;HaplotypeScore=1.30;MLEAC=4;MLEAF=0.667;MQ=58.54;MQ0=0;MQRankSum=1.29;QD=21.27;ReadPosRankSum=-1.212e+00;SB=-1.878e+03;VQSLOD=7.32;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:27,49:77:99:1466,0,733:127 1|1:0,64:64:99:1888,147,0:127 0|1:18,27:48:99:666,0,410:127 7 38984187 rs118081099 A C 569.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-1.100e-01;DB;DP=182;Dels=0.00;FS=6.20;HaplotypeScore=0.553;MLEAC=1;MLEAF=0.167;MQ=54.22;MQ0=0;MQRankSum=1.67;QD=9.33;ReadPosRankSum=1.16;SB=-1.260e+02;VQSLOD=4.89;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:72,0:72:99:0,196,2446:127 0|1:38,23:61:99:604,0,1196:127 0|0:48,1:49:99:0,138,1711:127 7 48862174 rs965346 A G 877.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-6.250e+00;DB;DP=194;Dels=0.00;FS=6.11;HaplotypeScore=0.649;MLEAC=1;MLEAF=0.167;MQ=57.54;MQ0=0;MQRankSum=2.06;QD=16.25;ReadPosRankSum=-1.204e+00;SB=-4.040e+02;VQSLOD=6.24;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:82,0:82:99:0,232,3007:127 0|0:58,0:58:99:0,160,2067:127 0|1:22,32:54:99:912,0,686:127 7 56584972 rs34475770 C T 2465.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-1.030e-01;DB;DP=255;Dels=0.00;FS=2.23;HaplotypeScore=0.884;MLEAC=2;MLEAF=0.333;MQ=58.76;MQ0=0;MQRankSum=1.77;QD=15.03;ReadPosRankSum=1.13;SB=-1.412e+03;VQSLOD=6.57;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:91,0:91:99:0,259,3369:127 0|1:36,49:85:99:1444,0,1000:127 0|1:38,41:79:99:1060,0,1084:127 7 62232046 . C T 1155.24 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.167;AN=6;BaseQRankSum=-2.643e+00;DP=230;Dels=0.00;FS=6.30;HaplotypeScore=12.77;MLEAC=1;MLEAF=0.167;MQ=58.61;MQ0=3;MQRankSum=-6.970e-01;QD=15.20;ReadPosRankSum=-1.202e+00;SB=-4.440e+02;VQSLOD=2.57;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|0:77,1:78:99:0,217,2824:127 0|0:76,0:76:99:0,202,2604:127 0|1:34,42:76:99:1190,0,994:127 7 69334430 rs917719 C T 1223.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=5.84;DB;DP=193;Dels=0.00;FS=6.66;HaplotypeScore=0.815;MLEAC=2;MLEAF=0.333;MQ=59.81;MQ0=0;MQRankSum=1.63;QD=9.63;ReadPosRankSum=1.46;SB=-7.370e+02;VQSLOD=7.00;culprit=MQ GT:AD:DP:GQ:PL:TP 1|0:38,39:77:99:770,0,1258:127 1|0:26,24:50:99:492,0,840:127 0|0:66,0:66:99:0,172,2210:127 7 79508376 rs2525826 G T 716.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=2.15;DB;DP=196;Dels=0.00;FS=0.00;HaplotypeScore=0.866;MLEAC=1;MLEAF=0.167;MQ=59.48;MQ0=0;MQRankSum=1.42;QD=13.51;ReadPosRankSum=0.263;SB=-4.080e+02;VQSLOD=9.57;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:65,0:65:99:0,181,2312:127 0|0:78,0:78:99:0,226,2916:127 0|1:27,26:53:99:751,0,845:127 7 89752110 rs39232 T G 3944.01 VQSRTrancheSNP99.00to99.90 AC=6;AF=1.00;AN=6;DB;DP=216;Dels=0.00;FS=0.00;HaplotypeScore=1.45;MLEAC=6;MLEAF=1.00;MQ=38.19;MQ0=21;QD=18.26;SB=-2.716e+03;VQSLOD=2.66;culprit=MQ GT:AD:DP:GQ:PL:TP 1|1:0,70:70:99:1564,132,0:101 1|1:0,79:79:99:1258,108,0:101 1|1:0,66:66:99:1122,102,0:101 7 101161506 rs2158739 C T 4522.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=1.70;DB;DP=172;Dels=0.00;FS=4.28;HaplotypeScore=1.51;MLEAC=5;MLEAF=0.833;MQ=58.18;MQ0=0;MQRankSum=-2.950e-01;QD=26.29;ReadPosRankSum=0.974;SB=-2.287e+03;VQSLOD=8.28;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,72:73:99:2443,202,0:110 1|0:23,26:50:99:711,0,586:110 1|1:0,48:49:99:1368,111,0:110 7 110843795 rs214455 A G 8548.01 PASS AC=6;AF=1.00;AN=6;DB;DP=258;Dels=0.00;FS=0.00;HaplotypeScore=2.36;MLEAC=6;MLEAF=1.00;MQ=59.35;MQ0=0;QD=33.13;SB=-4.197e+03;VQSLOD=10.76;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,106:106:99:3535,301,0:127 1|1:0,66:66:99:2270,193,0:127 1|1:0,86:86:99:2743,229,0:127 7 124589684 rs12113765 G C 4948.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-2.607e+00;DB;DP=243;Dels=0.00;FS=1.04;HaplotypeScore=3.38;MLEAC=4;MLEAF=0.667;MQ=58.74;MQ0=0;MQRankSum=1.25;QD=20.36;ReadPosRankSum=-3.870e-01;SB=-2.411e+03;VQSLOD=7.05;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:44,27:71:99:796,0,1350:127 1|1:0,84:85:99:2760,217,0:127 0|1:41,46:87:99:1392,0,1180:127 7 134269995 rs67235184 G GA 2917.20 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=0.835;DB;DP=219;FS=1.09;HaplotypeScore=39.14;MLEAC=3;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=-3.700e-02;QD=19.19;RPA=7,8;RU=A;ReadPosRankSum=-9.210e-01;SB=-1.316e+03;STR;VQSLOD=5.11;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:51,33:84:99:916,0,1151:127 1|1:2,65:68:99:2055,192,0:127 0|0:65,0:67:99:0,186,2051:127 7 144383888 rs73161092 T C 689.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-7.434e+00;DB;DP=254;Dels=0.00;FS=8.63;HaplotypeScore=0.00;MLEAC=1;MLEAF=0.167;MQ=59.54;MQ0=0;MQRankSum=0.163;QD=8.62;ReadPosRankSum=-1.802e+00;SB=-3.560e+02;VQSLOD=6.45;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|0:90,0:90:99:0,268,3553:127 0|1:47,33:80:99:724,0,1392:127 0|0:84,0:84:99:0,202,2644:127 7 152208470 rs6464236 G C 4321.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=5.23;DB;DP=169;Dels=0.00;FS=1.63;HaplotypeScore=1.36;MLEAC=5;MLEAF=0.833;MQ=57.18;MQ0=1;MQRankSum=1.91;QD=25.57;ReadPosRankSum=0.892;SB=-2.137e+03;VQSLOD=6.76;culprit=MQ GT:AD:DP:GQ:PL:TP 1|1:1,56:57:99:1949,150,0:122 1|1:0,54:54:99:1557,123,0:122 1|0:30,28:58:99:815,0,715:122 7 158686803 rs55765467 T C 200.26 VQSRTrancheSNP99.00to99.90 AC=3;AF=0.500;AN=6;BaseQRankSum=-1.011e+01;DB;DP=310;Dels=0.00;FS=2.60;HaplotypeScore=1.28;MLEAC=3;MLEAF=0.500;MQ=47.32;MQ0=0;MQRankSum=-4.959e+00;QD=0.650;ReadPosRankSum=-1.096e+01;SB=-1.206e+03;VQSLOD=-1.764e+01;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 0/1:64,33:97:99:148,0,1949:32 0/1:73,45:118:58:58,0,2287:32 0/1:65,30:95:33:33,0,1910:32 8 4048009 rs7007410 C T 2713.26 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=0.954;DB;DP=197;Dels=0.00;FS=2.48;HaplotypeScore=0.712;MLEAC=3;MLEAF=0.500;MQ=57.03;MQ0=0;MQRankSum=0.882;QD=13.77;ReadPosRankSum=-4.960e-01;SB=-1.406e+03;VQSLOD=6.50;culprit=FS GT:AD:DP:GQ:PL:TP 0/1:38,30:68:99:847,0,1168:127 0/1:30,30:60:99:916,0,921:127 0/1:32,36:69:99:989,0,882:127 8 8974322 rs28440961 G A 1682.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.72;DB;DP=190;Dels=0.00;FS=0.579;HaplotypeScore=1.54;MLEAC=2;MLEAF=0.333;MQ=59.33;MQ0=0;MQRankSum=-6.520e-01;QD=12.65;ReadPosRankSum=0.746;SB=-7.040e+02;VQSLOD=9.37;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 1|0:32,32:64:99:790,0,1002:125 1|0:33,36:69:99:931,0,866:125 0|0:57,0:57:99:0,126,1622:125 8 14463368 rs1355302 T A 2523.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=6.79;DB;DP=236;Dels=0.00;FS=3.78;HaplotypeScore=0.324;MLEAC=2;MLEAF=0.333;MQ=59.14;MQ0=0;MQRankSum=-3.810e-01;QD=15.97;ReadPosRankSum=-4.500e-02;SB=-1.421e+03;VQSLOD=7.69;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|1:36,43:79:99:1332,0,1176:127 0|0:78,0:78:99:0,214,2749:127 1|0:35,44:79:99:1230,0,1162:127 8 21736923 rs13256921 G A 217.24 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.167;AN=6;BaseQRankSum=1.88;DB;DP=93;Dels=0.00;FS=5.53;HaplotypeScore=6.50;MLEAC=1;MLEAF=0.167;MQ=42.13;MQ0=3;MQRankSum=0.517;QD=6.79;ReadPosRankSum=1.71;SB=-1.980e+02;VQSLOD=-2.643e+00;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|0:34,0:34:66:0,66,691:41 0|1:15,17:32:99:252,0,211:41 0|0:27,0:27:42:0,42,425:41 8 30862954 rs149290124 C CA 3883 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-1.321e+00;DB;DP=261;FS=0.755;HaplotypeScore=37.27;MLEAC=5;MLEAF=0.833;MQ=58.08;MQ0=0;MQRankSum=0.330;QD=14.88;RPA=11,12;RU=A;ReadPosRankSum=-5.780e-01;SB=-1.926e+03;STR;VQSLOD=5.37;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:21,76:105:99:1980,179,0:91 1|0:51,22:75:99:597,0,485:91 1|1:24,54:81:92:1306,92,0:91 8 42044954 rs1058720 G A 2760.25 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=4.31;DB;DP=157;Dels=0.00;FS=0.00;HaplotypeScore=2.10;MLEAC=4;MLEAF=0.667;MQ=58.82;MQ0=0;MQRankSum=-2.021e+00;QD=17.58;ReadPosRankSum=-4.620e-01;SB=-1.377e+03;VQSLOD=7.58;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,56:56:99:1820,147,0:127 1|0:24,27:51:99:555,0,233:127 1|0:26,24:50:99:427,0,458:127 8 56608897 rs57623198 C T 1911.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-1.515e+00;DB;DP=229;Dels=0.00;FS=0.00;HaplotypeScore=1.13;MLEAC=2;MLEAF=0.333;MQ=59.80;MQ0=0;MQRankSum=0.336;QD=12.66;ReadPosRankSum=-2.326e+00;SB=-9.730e+02;VQSLOD=8.56;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:78,0:78:99:0,229,2989:127 0|1:44,30:74:99:897,0,1444:127 0|1:44,33:77:99:1053,0,1400:127 8 66327344 rs13282622 G A 3918.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=4.51;DB;DP=192;Dels=0.00;FS=3.53;HaplotypeScore=1.65;MLEAC=4;MLEAF=0.667;MQ=58.91;MQ0=0;MQRankSum=0.706;QD=20.41;ReadPosRankSum=-3.270e-01;SB=-2.091e+03;VQSLOD=8.63;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:34,37:71:99:1137,0,923:127 0|1:32,28:61:99:806,0,988:127 1|1:0,60:60:99:1975,153,0:127 8 78181000 rs1563030 A G 5178.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-3.000e-02;DB;DP=192;Dels=0.00;FS=4.68;HaplotypeScore=2.95;MLEAC=5;MLEAF=0.833;MQ=59.62;MQ0=0;MQRankSum=-4.670e-01;QD=26.97;ReadPosRankSum=-8.550e-01;SB=-2.617e+03;VQSLOD=7.34;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:0,59:59:99:1954,150,0:127 1|0:32,37:70:99:1198,0,888:127 1|1:0,63:63:99:2026,156,0:127 8 90278211 rs11998540 A T 357.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-1.457e+00;DB;DP=69;Dels=0.00;FS=1.29;HaplotypeScore=0.00;MLEAC=2;MLEAF=0.333;MQ=58.96;MQ0=0;MQRankSum=1.41;QD=8.12;ReadPosRankSum=1.26;SB=-9.501e+01;VQSLOD=5.96;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|1:12,7:19:99:185,0,416:60 0|0:25,0:25:60:0,60,805:60 1|0:16,9:25:99:211,0,500:60 8 102355800 rs10103956 G T 1756.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=0.927;DB;DP=189;Dels=0.00;FS=5.92;HaplotypeScore=1.54;MLEAC=2;MLEAF=0.333;MQ=59.66;MQ0=0;MQRankSum=-4.200e-01;QD=13.41;ReadPosRankSum=-1.900e-02;SB=-5.470e+02;VQSLOD=8.16;culprit=MQ GT:AD:DP:GQ:PL:TP 1|0:32,38:70:99:1078,0,999:127 1|0:35,26:61:99:717,0,1103:127 0|0:57,0:58:99:0,156,2011:127 8 113376378 rs41340951 T C 4379.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-8.019e+00;DB;DP=211;Dels=0.00;FS=1.83;HaplotypeScore=0.263;MLEAC=4;MLEAF=0.667;MQ=59.85;MQ0=0;MQRankSum=1.27;QD=20.75;ReadPosRankSum=0.144;SB=-1.893e+03;VQSLOD=8.84;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:0,67:67:99:2221,187,0:127 1|0:32,37:69:99:1083,0,1066:127 1|0:35,40:75:99:1075,0,1108:127 8 123499998 rs9693135 T C 926.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-7.820e+00;DB;DP=207;Dels=0.00;FS=2.68;HaplotypeScore=1.26;MLEAC=2;MLEAF=0.333;MQ=56.08;MQ0=0;MQRankSum=-2.729e+00;QD=6.34;ReadPosRankSum=-2.690e-01;SB=-8.230e+02;VQSLOD=4.30;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:61,0:61:99:0,172,2301:127 0|1:37,35:72:99:622,0,769:127 0|1:48,26:74:99:343,0,1280:127 8 132727531 rs7000409 G A 2050.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=5.47;DB;DP=220;Dels=0.00;FS=5.20;HaplotypeScore=1.94;MLEAC=2;MLEAF=0.333;MQ=59.71;MQ0=0;MQRankSum=1.23;QD=14.14;ReadPosRankSum=-8.710e-01;SB=-1.080e+03;VQSLOD=7.79;culprit=MQ GT:AD:DP:GQ:PL:TP 0|1:29,35:64:99:1215,0,785:127 0|0:75,0:75:99:0,190,2423:127 1|0:50,31:81:99:874,0,1611:127 8 140651779 rs1469039 G A 1879.26 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-2.189e+00;DB;DP=145;Dels=0.00;FS=0.00;HaplotypeScore=1.77;MLEAC=3;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=0.745;QD=12.96;ReadPosRankSum=-1.590e-01;SB=-9.360e+02;VQSLOD=9.01;culprit=FS GT:AD:DP:GQ:PL:TP 0/1:23,24:47:99:612,0,740:127 0/1:21,31:52:99:684,0,478:127 0/1:20,26:46:99:622,0,367:127 9 2072356 rs4741641 T G 2054.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-7.235e+00;DB;DP=243;Dels=0.00;FS=0.00;HaplotypeScore=2.21;MLEAC=2;MLEAF=0.333;MQ=59.64;MQ0=0;MQRankSum=1.17;QD=13.00;ReadPosRankSum=-4.750e-01;SB=-1.004e+03;VQSLOD=9.02;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:49,45:94:99:1245,0,1615:127 0|0:85,0:85:99:0,217,2818:127 1|0:32,32:64:99:848,0,936:127 9 9066127 rs57751104 ATATT A 4412 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-8.800e-02;DB;DP=214;FS=8.47;HaplotypeScore=16.59;MLEAC=2;MLEAF=0.333;MQ=58.75;MQ0=0;MQRankSum=0.462;QD=29.61;RPA=2,1;RU=TATT;ReadPosRankSum=1.38;SB=-1.837e+03;STR;VQSLOD=4.42;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:41,36:79:99:2129,0,2123:127 1|0:32,38:70:99:2283,0,1679:127 0|0:65,0:65:99:0,184,4023:127 9 16302655 rs9298755 T G 1394.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=3.36;DB;DP=200;Dels=0.00;FS=0.00;HaplotypeScore=3.19;MLEAC=2;MLEAF=0.333;MQ=59.33;MQ0=0;MQRankSum=0.586;QD=10.03;ReadPosRankSum=-7.710e-01;SB=-8.720e+02;VQSLOD=7.77;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|0:60,1:61:99:0,165,2004:127 0|1:29,28:57:99:494,0,759:127 0|1:41,40:82:99:939,0,1069:127 9 25201692 rs9408058 C T 8643.01 PASS AC=6;AF=1.00;AN=6;DB;DP=245;Dels=0.00;FS=0.00;HaplotypeScore=0.898;MLEAC=6;MLEAF=1.00;MQ=59.13;MQ0=0;QD=35.28;SB=-4.398e+03;VQSLOD=12.17;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,89:89:99:3312,256,0:127 1|1:0,81:81:99:2771,223,0:127 1|1:0,75:75:99:2560,202,0:127 9 33446281 . C CT 31.72 VQSRTrancheINDEL99.90to100.00 AC=1;AF=0.167;AN=6;BaseQRankSum=-2.119e+00;DP=178;FS=127.57;HaplotypeScore=21.55;MLEAC=1;MLEAF=0.167;MQ=58.69;MQ0=0;MQRankSum=1.61;QD=0.620;RPA=2,3;RU=T;ReadPosRankSum=-5.268e+00;SB=-4.493e+00;STR;VQSLOD=-1.057e+01;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:77,0:79:73:0,73,2094:6 0|0:46,0:48:5:0,5,958:6 0|1:35,15:51:75:75,0,1073:6 9 44998848 . C G 254.43 VQSRTrancheSNP99.00to99.90 AC=5;AF=0.833;AN=6;BaseQRankSum=2.20;DP=193;Dels=0.00;FS=10.82;HaplotypeScore=0.245;MLEAC=5;MLEAF=0.833;MQ=6.48;MQ0=163;MQRankSum=-1.206e+00;QD=1.32;ReadPosRankSum=0.790;SB=-1.372e+02;VQSLOD=-6.632e+00;culprit=QD GT:AD:DP:GQ:PL:TP 1|0:39,27:66:23:132,0,23:8 1|1:36,16:52:15:118,15,0:8 0|1:53,22:75:1:45,6,0:8 9 69810010 rs113063015 A C 280.26 VQSRTrancheSNP99.90to100.00 AC=3;AF=0.500;AN=6;BaseQRankSum=-1.223e+00;DB;DP=716;DS;Dels=0.00;FS=9.00;HaplotypeScore=39.83;MLEAC=3;MLEAF=0.500;MQ=37.32;MQ0=64;MQRankSum=-3.574e+00;QD=0.390;ReadPosRankSum=-8.970e-01;SB=-1.065e-02;VQSLOD=-6.817e+01;culprit=DP GT:AD:DP:GQ:PL:TP 0/1:218,23:241:73:73,0,3591:70 0/1:188,39:227:99:172,0,4233:70 0/1:217,31:248:74:74,0,5042:70 9 78741390 rs7049138 G A 1797.24 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=6.24;DB;DP=168;Dels=0.00;FS=4.00;HaplotypeScore=1.09;MLEAC=3;MLEAF=0.500;MQ=55.32;MQ0=2;MQRankSum=-1.673e+00;QD=16.34;ReadPosRankSum=-6.260e-01;SB=-7.740e+02;VQSLOD=5.19;culprit=MQ GT:AD:DP:GQ:PL:TP 1|0:37,33:70:99:828,0,918:80 1|1:0,40:40:81:1014,81,0:80 0|0:58,0:58:99:0,129,1403:80 9 89010476 rs164937 T C 736.24 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.167;AN=6;BaseQRankSum=-3.977e+00;DB;DP=216;Dels=0.00;FS=1.48;HaplotypeScore=1.06;MLEAC=1;MLEAF=0.167;MQ=39.79;MQ0=9;MQRankSum=-3.028e+00;QD=9.56;ReadPosRankSum=0.542;SB=-4.240e+02;VQSLOD=2.08;culprit=MQ GT:AD:DP:GQ:PL:TP 0|0:66,0:66:99:0,174,2097:127 0|1:40,37:77:99:771,0,876:127 0|0:73,0:73:99:0,183,2147:127 9 98491693 rs12337935 C A 1474.25 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=2.10;DB;DP=97;Dels=0.00;FS=14.28;HaplotypeScore=1.77;MLEAC=4;MLEAF=0.667;MQ=58.64;MQ0=0;MQRankSum=-2.240e-01;QD=15.20;ReadPosRankSum=1.17;SB=-6.430e+02;VQSLOD=5.80;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:14,12:26:99:348,0,352:63 1|1:0,28:29:63:781,63,0:63 0|1:17,25:42:99:387,0,364:63 9 109619207 rs4743032 A T 3810.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-2.859e+00;DB;DP=214;Dels=0.00;FS=10.28;HaplotypeScore=0.322;MLEAC=3;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.557;QD=25.07;ReadPosRankSum=-8.360e-01;SB=-2.019e+03;VQSLOD=8.14;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:37,39:76:99:1185,0,1225:127 1|1:0,76:76:99:2625,202,0:127 0|0:62,0:62:99:0,156,2049:127 9 118670009 rs66523513 CT C 5633 PASS AC=6;AF=1.00;AN=6;BaseQRankSum=-6.600e-02;DB;DP=222;FS=6.40;HaplotypeScore=30.72;MLEAC=6;MLEAF=1.00;MQ=59.97;MQ0=0;MQRankSum=0.490;QD=25.37;RPA=11,10;RU=T;ReadPosRankSum=2.43;SB=-2.667e+03;STR;VQSLOD=3.39;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:6,71:78:99:2079,216,0:120 1|1:10,54:65:99:1524,120,0:120 1|1:9,69:79:99:2030,209,0:120 9 130235282 . A G 166.26 VQSRTrancheSNP99.90to100.00 AC=2;AF=0.333;AN=6;BaseQRankSum=-8.543e+00;DP=232;Dels=0.00;FS=233.04;HaplotypeScore=3.00;MLEAC=2;MLEAF=0.333;MQ=59.04;MQ0=0;MQRankSum=-2.038e+00;QD=1.15;ReadPosRankSum=-7.649e+00;SB=-3.100e-03;VQSLOD=-1.398e+02;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:74,14:88:99:0,108,2160:59 0|1:42,36:79:60:60,0,966:59 0|1:47,18:65:99:145,0,922:59 9 138617823 rs55724592 C T 53.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-3.800e-01;DB;DP=72;Dels=0.00;FS=8.08;HaplotypeScore=1.02;MLEAC=1;MLEAF=0.167;MQ=58.90;MQ0=0;MQRankSum=0.851;QD=2.66;ReadPosRankSum=-3.440e-01;SB=-9.096e+01;VQSLOD=4.27;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:20,0:20:48:0,48,580:44 0|0:32,0:32:48:0,48,577:44 0|1:10,10:20:88:88,0,199:44 10 4588547 rs313427 C T 1985.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=3.69;DB;DP=204;Dels=0.00;FS=1.81;HaplotypeScore=0.614;MLEAC=2;MLEAF=0.333;MQ=59.73;MQ0=0;MQRankSum=0.241;QD=14.18;ReadPosRankSum=0.717;SB=-1.082e+03;VQSLOD=9.78;culprit=MQ GT:AD:DP:GQ:PL:TP 1|0:39,35:74:99:1029,0,1182:127 1|0:32,34:66:99:995,0,1024:127 0|0:64,0:64:99:0,175,2242:127 10 11560326 rs4424580 C T 1027.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-1.780e-01;DB;DP=207;Dels=0.00;FS=0.573;HaplotypeScore=2.20;MLEAC=2;MLEAF=0.333;MQ=59.24;MQ0=0;MQRankSum=-9.880e-01;QD=7.78;ReadPosRankSum=-4.920e-01;SB=-7.450e+02;VQSLOD=8.46;culprit=QD GT:AD:DP:GQ:PL:TP 1|0:41,32:73:99:609,0,930:96 1|0:29,30:59:99:457,0,570:96 0|0:74,1:75:96:0,96,1185:96 10 19567676 rs61458006 G T 599.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-2.610e+00;DB;DP=195;Dels=0.00;FS=0.844;HaplotypeScore=0.879;MLEAC=1;MLEAF=0.167;MQ=59.57;MQ0=0;MQRankSum=-1.910e-01;QD=11.31;ReadPosRankSum=-1.635e+00;SB=-2.780e+02;VQSLOD=9.36;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:75,0:75:99:0,208,2645:127 0|1:30,23:53:99:634,0,915:127 0|0:67,0:67:99:0,199,2540:127 10 29082980 . G C 42.53 VQSRTrancheSNP99.00to99.90 AC=3;AF=0.500;AN=6;BaseQRankSum=-1.216e+00;DP=107;Dels=0.00;FS=60.98;HaplotypeScore=1.09;MLEAC=3;MLEAF=0.500;MQ=55.72;MQ0=0;MQRankSum=-6.330e-01;QD=0.400;ReadPosRankSum=-4.307e+00;SB=-2.798e-01;VQSLOD=-1.117e+01;culprit=FS GT:AD:DP:GQ:PL:TP 0/1:30,12:43:12:12,0,757:12 0/1:19,11:30:35:35,0,429:12 0/1:25,9:34:34:34,0,388:12 10 38560911 rs80189231 T A 1072.26 VQSRTrancheSNP99.00to99.90 AC=3;AF=0.500;AN=6;BaseQRankSum=0.103;DB;DP=356;Dels=0.00;FS=12.04;HaplotypeScore=5.40;MLEAC=3;MLEAF=0.500;MQ=49.74;MQ0=6;MQRankSum=-2.686e+00;QD=3.01;ReadPosRankSum=0.797;SB=-1.690e+02;VQSLOD=-3.513e+00;culprit=QD GT:AD:DP:GQ:PL:TP 0/1:109,26:135:99:389,0,2879:127 0/1:84,27:111:99:539,0,2214:127 0/1:93,17:110:99:183,0,2277:127 10 46605359 . CT C 883.20 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=1.62;DP=136;FS=9.66;HaplotypeScore=4.70;MLEAC=3;MLEAF=0.500;MQ=22.12;MQ0=1;MQRankSum=0.368;QD=8.57;RPA=7,6;RU=T;ReadPosRankSum=-1.076e+00;SB=-1.190e+02;STR;VQSLOD=2.55;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:33,0:32:90:0,90,1016:25 0|1:66,15:81:99:303,0,1810:25 0|1:2,19:20:0:634,54,0:25 10 56495833 rs6481118 G A 7633.01 PASS AC=6;AF=1.00;AN=6;DB;DP=212;Dels=0.00;FS=0.00;HaplotypeScore=0.333;MLEAC=6;MLEAF=1.00;MQ=54.64;MQ0=0;QD=36.00;SB=-2.091e+03;VQSLOD=8.67;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,62:62:99:2383,184,0:127 1|1:1,67:68:99:2375,184,0:127 1|1:0,82:82:99:2875,223,0:127 10 65355538 rs10733794 A G 2464.24 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-8.392e+00;DB;DP=193;Dels=0.00;FS=7.47;HaplotypeScore=2.54;MLEAC=3;MLEAF=0.500;MQ=58.06;MQ0=2;MQRankSum=0.999;QD=18.96;ReadPosRankSum=-1.229e+00;SB=-1.065e+03;VQSLOD=6.39;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:33,32:65:99:830,0,1039:127 1|1:1,64:65:99:1679,153,0:127 0|0:63,0:63:99:0,159,2042:127 10 74020452 rs72806301 C A 1116.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-2.155e+00;DB;DP=135;Dels=0.00;FS=3.28;HaplotypeScore=0.872;MLEAC=2;MLEAF=0.333;MQ=58.76;MQ0=0;MQRankSum=-8.180e-01;QD=11.88;ReadPosRankSum=1.48;SB=-6.800e+02;VQSLOD=7.27;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 0|1:20,27:47:99:658,0,446:104 0|0:41,0:41:99:0,105,1324:104 1|0:25,22:47:99:497,0,482:104 10 85258657 rs4454662 C A 7638.01 PASS AC=6;AF=1.00;AN=6;BaseQRankSum=1.72;DB;DP=223;Dels=0.00;FS=4.52;HaplotypeScore=1.13;MLEAC=6;MLEAF=1.00;MQ=58.32;MQ0=0;MQRankSum=-1.230e+00;QD=34.25;ReadPosRankSum=1.15;SB=-2.841e+03;VQSLOD=7.65;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:1,64:65:99:2156,169,0:127 1|1:0,89:89:99:2982,238,0:127 1|1:0,69:69:99:2500,196,0:127 10 95435201 rs2422323 C T 4017.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=6.44;DB;DP=203;Dels=0.00;FS=13.13;HaplotypeScore=3.24;MLEAC=4;MLEAF=0.667;MQ=55.24;MQ0=0;MQRankSum=1.17;QD=19.79;ReadPosRankSum=-6.550e-01;SB=-2.177e+03;VQSLOD=4.60;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:38,45:83:99:1327,0,931:127 1|1:1,63:64:99:1966,156,0:127 0|1:30,25:56:99:724,0,807:127 10 106444111 rs72813617 A G 632.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-8.380e-01;DB;DP=197;Dels=0.00;FS=4.12;HaplotypeScore=1.82;MLEAC=1;MLEAF=0.167;MQ=59.35;MQ0=0;MQRankSum=-1.142e+00;QD=12.40;ReadPosRankSum=-1.947e+00;SB=-2.390e+02;VQSLOD=7.62;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 0|0:84,0:84:99:0,241,3129:127 0|0:62,0:62:99:0,159,2008:127 0|1:27,24:51:99:667,0,584:127 10 116646860 rs4752347 T A 4159.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-3.459e+00;DB;DP=197;Dels=0.00;FS=3.52;HaplotypeScore=0.631;MLEAC=4;MLEAF=0.667;MQ=59.27;MQ0=0;MQRankSum=1.05;QD=21.11;ReadPosRankSum=-1.271e+00;SB=-2.347e+03;VQSLOD=8.33;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 1|1:0,63:63:99:2191,169,0:127 1|0:31,35:66:99:1031,0,863:127 1|0:31,37:68:99:937,0,774:127 10 125452232 rs7900707 A G 3211.24 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-6.610e+00;DB;DP=189;Dels=0.00;FS=17.74;HaplotypeScore=0.00;MLEAC=4;MLEAF=0.667;MQ=59.66;MQ0=0;MQRankSum=0.614;QD=16.99;ReadPosRankSum=-3.210e-01;SB=-1.553e+03;VQSLOD=6.90;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:0,61:61:99:1944,168,0:127 1|0:44,26:70:99:627,0,1357:127 1|0:29,29:58:99:682,0,862:127 10 132949760 rs10829924 A C 684.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-2.328e+00;DB;DP=215;Dels=0.00;FS=15.46;HaplotypeScore=1.32;MLEAC=1;MLEAF=0.167;MQ=59.70;MQ0=0;MQRankSum=-1.053e+00;QD=10.53;ReadPosRankSum=-2.893e+00;SB=-2.920e+02;VQSLOD=5.89;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 0|0:80,0:81:99:0,229,2999:127 0|0:69,0:69:99:0,175,2268:127 0|1:35,30:65:99:719,0,1046:127 11 3839556 rs5789310 CA C 803.10 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=0.138;DB;DP=170;FS=4.50;HaplotypeScore=36.64;MLEAC=3;MLEAF=0.500;MQ=55.95;MQ0=2;MQRankSum=2.28;QD=4.72;RPA=17,16;RU=A;ReadPosRankSum=3.21;SB=-3.839e+02;STR;VQSLOD=1.81;culprit=QD GT:AD:DP:GQ:PL:TP 0/1:35,17:55:32:329,0,32:3 0/1:45,9:57:8:276,0,8:3 0/1:30,19:52:1:244,0,1:3 11 10741836 rs72853043 G A 175.24 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.167;AN=6;BaseQRankSum=0.127;DB;DP=174;Dels=0.00;FS=7.09;HaplotypeScore=7.46;MLEAC=1;MLEAF=0.167;MQ=55.72;MQ0=1;MQRankSum=-1.291e+00;QD=3.44;ReadPosRankSum=-1.185e+00;SB=-2.220e+02;VQSLOD=1.61;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:78,0:78:99:0,105,1278:65 0|0:42,0:45:66:0,66,802:65 0|1:21,29:51:99:210,0,469:65 11 19325064 rs793250 G A 5752.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=5.08;DB;DP=203;Dels=0.00;FS=2.53;HaplotypeScore=0.817;MLEAC=5;MLEAF=0.833;MQ=59.35;MQ0=0;MQRankSum=-6.100e-02;QD=28.34;ReadPosRankSum=0.095;SB=-3.093e+03;VQSLOD=9.46;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,71:71:99:2527,190,0:127 1|1:0,78:78:99:2626,205,0:127 1|0:32,22:54:99:599,0,768:127 11 26026566 rs7942277 T C 5414.01 PASS AC=6;AF=1.00;AN=6;DB;DP=176;Dels=0.00;FS=0.00;HaplotypeScore=0.245;MLEAC=6;MLEAF=1.00;MQ=58.89;MQ0=0;QD=30.76;SB=-2.812e+03;VQSLOD=11.05;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:0,53:53:99:1707,132,0:122 1|1:0,53:53:99:1581,123,0:122 1|1:0,70:70:99:2126,163,0:122 11 35980461 rs263087 A T 3494.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-7.010e-01;DB;DP=186;Dels=0.00;FS=0.00;HaplotypeScore=2.96;MLEAC=4;MLEAF=0.667;MQ=59.34;MQ0=0;MQRankSum=0.836;QD=18.79;ReadPosRankSum=7.000e-03;SB=-1.535e+03;VQSLOD=7.64;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|1:36,35:71:99:1001,0,1165:127 0|1:30,26:56:99:710,0,796:127 1|1:0,59:59:99:1783,144,0:127 11 44985620 rs7106313 C T 338.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=2.18;DB;DP=162;Dels=0.00;FS=4.84;HaplotypeScore=2.00;MLEAC=1;MLEAF=0.167;MQ=56.94;MQ0=0;MQRankSum=2.02;QD=8.67;ReadPosRankSum=0.983;SB=-2.190e+02;VQSLOD=6.66;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:79,0:80:99:0,174,2084:72 0|0:43,0:43:72:0,72,877:72 0|1:20,18:39:99:373,0,365:72 11 55040918 rs187118824 A T 1019.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.08;DB;DP=65;Dels=0.020;FS=12.72;HaplotypeScore=0.977;MLEAC=2;MLEAF=0.333;MQ=56.64;MQ0=1;MQRankSum=0.323;QD=25.48;ReadPosRankSum=0.873;SB=-2.060e+01;VQSLOD=4.42;culprit=DP GT:AD:DP:GQ:PL:TP 0|1:2,9:11:48:325,0,48:50 0|0:24,1:25:63:0,63,833:50 1|0:6,22:28:51:733,0,51:50 11 65339346 rs1194104 C T 1804.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-2.465e+00;DB;DP=189;Dels=0.00;FS=8.43;HaplotypeScore=2.27;MLEAC=2;MLEAF=0.333;MQ=59.31;MQ0=0;MQRankSum=-1.200e-01;QD=13.67;ReadPosRankSum=-3.060e-01;SB=-1.061e+03;VQSLOD=7.95;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:57,0:57:99:0,157,2050:127 0|1:30,35:65:99:781,0,822:127 0|1:23,44:67:99:1062,0,690:127 11 75978490 rs655877 G C 2986.25 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-8.460e-01;DB;DP=127;Dels=0.00;FS=5.43;HaplotypeScore=0.263;MLEAC=5;MLEAF=0.833;MQ=59.42;MQ0=0;MQRankSum=0.026;QD=23.51;ReadPosRankSum=0.168;SB=-1.613e+03;VQSLOD=7.04;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:0,50:50:99:1405,111,0:101 1|1:0,45:46:99:1269,102,0:101 1|0:17,14:31:99:354,0,469:101 11 86061661 rs11825046 T C 6014.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-3.250e+00;DB;DP=282;Dels=0.00;FS=0.960;HaplotypeScore=1.64;MLEAC=4;MLEAF=0.667;MQ=59.57;MQ0=0;MQRankSum=1.06;QD=21.33;ReadPosRankSum=-1.763e+00;SB=-3.081e+03;VQSLOD=7.35;culprit=DP GT:AD:DP:GQ:PL:TP 1|0:54,49:103:99:1498,0,1848:127 1|1:0,83:83:99:2924,223,0:127 0|1:44,52:96:99:1592,0,1380:127 11 96559202 rs72048706 C CAA 373.24 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-7.960e-01;DB;DP=121;FS=1.54;HaplotypeScore=64.55;MLEAC=4;MLEAF=0.667;MQ=39.96;MQ0=6;MQRankSum=-5.390e-01;QD=3.08;RPA=21,23;RU=A;ReadPosRankSum=-3.583e+00;SB=-1.985e+02;STR;VQSLOD=1.31;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 1|0:20,8:32:24:111,0,24:22 1|1:40,0:41:29:180,29,0:22 0|1:39,0:39:41:133,0,41:22 11 103989190 rs1545865 T C 4915.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-4.030e+00;DB;DP=219;Dels=0.00;FS=1.23;HaplotypeScore=1.21;MLEAC=4;MLEAF=0.667;MQ=59.37;MQ0=0;MQRankSum=1.10;QD=22.44;ReadPosRankSum=0.773;SB=-2.213e+03;VQSLOD=8.91;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 0|1:23,40:63:99:1203,0,669:127 0|1:36,52:88:99:1433,0,1136:127 1|1:0,68:68:99:2279,178,0:127 11 113825129 rs1150234 G A 2441.26 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=3.98;DB;DP=210;Dels=0.00;FS=0.00;HaplotypeScore=2.07;MLEAC=3;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=0.877;QD=11.63;ReadPosRankSum=0.262;SB=-1.513e+03;VQSLOD=9.04;culprit=FS GT:AD:DP:GQ:PL:TP 0/1:30,33:63:99:881,0,774:127 0/1:46,33:80:99:726,0,1020:127 0/1:32,35:67:99:873,0,759:127 11 123470819 rs1148095 T C 6964.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-8.500e-01;DB;DP=242;Dels=0.00;FS=1.48;HaplotypeScore=1.39;MLEAC=5;MLEAF=0.833;MQ=59.25;MQ0=0;MQRankSum=-1.734e+00;QD=28.78;ReadPosRankSum=-7.490e-01;SB=-3.242e+03;VQSLOD=8.79;culprit=MQRankSum GT:AD:DP:GQ:PL:TP 1|1:0,92:92:99:3408,265,0:127 1|0:35,51:86:99:1520,0,1059:127 1|1:0,64:64:99:2036,157,0:127 11 132780959 rs61906922 C T 1342.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=6.22;DB;DP=263;Dels=0.00;FS=0.601;HaplotypeScore=1.84;MLEAC=1;MLEAF=0.167;MQ=59.58;MQ0=0;MQRankSum=0.997;QD=15.25;ReadPosRankSum=-7.460e-01;SB=-6.890e+02;VQSLOD=8.81;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 0|0:87,0:87:99:0,250,2877:127 0|0:87,0:88:99:0,253,3009:127 0|1:43,45:88:99:1377,0,1138:127 12 5922552 rs17786352 C G 1874.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-7.386e+00;DB;DP=231;Dels=0.00;FS=0.00;HaplotypeScore=0.305;MLEAC=2;MLEAF=0.333;MQ=54.49;MQ0=0;MQRankSum=2.66;QD=13.11;ReadPosRankSum=1.04;SB=-9.400e+02;VQSLOD=4.75;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:44,35:79:99:897,0,1383:127 1|0:28,36:64:99:1016,0,734:127 0|0:88,0:88:99:0,238,3004:127 12 12560642 rs10772559 G T 501.28 VQSRTrancheSNP99.00to99.90 AC=4;AF=0.667;AN=6;BaseQRankSum=0.747;DB;DP=229;Dels=0.040;FS=17.41;HaplotypeScore=19.70;MLEAC=4;MLEAF=0.667;MQ=49.37;MQ0=0;MQRankSum=-3.656e+00;QD=2.19;ReadPosRankSum=-5.397e+00;SB=-2.196e+03;VQSLOD=-1.020e+01;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 1|1:0,66:66:24:273,24,0:24 1|0:29,45:74:99:148,0,702:24 1|0:33,46:80:99:122,0,781:24 12 21328424 rs4149040 G C 2565.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=0.888;DB;DP=252;Dels=0.00;FS=9.75;HaplotypeScore=0.608;MLEAC=2;MLEAF=0.333;MQ=59.49;MQ0=0;MQRankSum=1.17;QD=15.18;ReadPosRankSum=0.966;SB=-1.181e+03;VQSLOD=7.55;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:40,49:89:99:1534,0,1308:127 0|0:83,0:83:99:0,241,3117:127 1|0:45,35:80:99:1070,0,1402:127 12 29935607 rs7305813 A C 810.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=0.307;DB;DP=203;Dels=0.00;FS=14.33;HaplotypeScore=1.98;MLEAC=1;MLEAF=0.167;MQ=59.57;MQ0=0;MQRankSum=-1.640e-01;QD=12.86;ReadPosRankSum=-7.330e-01;SB=-2.950e+02;VQSLOD=7.90;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:71,0:71:99:0,193,2479:127 0|0:69,0:69:99:0,196,2464:127 0|1:28,35:63:99:845,0,847:127 12 39118960 rs79977305 G A 1330.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=6.31;DB;DP=263;Dels=0.00;FS=0.597;HaplotypeScore=1.46;MLEAC=1;MLEAF=0.167;MQ=58.83;MQ0=0;MQRankSum=1.92;QD=13.57;ReadPosRankSum=-5.480e-01;SB=-7.360e+02;VQSLOD=7.37;culprit=MQRankSum GT:AD:DP:GQ:PL:TP 0|0:81,0:81:99:0,241,2869:127 0|0:84,0:84:99:0,229,2712:127 0|1:51,47:98:99:1365,0,1343:127 12 48120010 rs3829317 A C 4015.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=1.66;DB;DP=162;Dels=0.00;FS=1.83;HaplotypeScore=2.18;MLEAC=5;MLEAF=0.833;MQ=59.48;MQ0=0;MQRankSum=0.154;QD=24.78;ReadPosRankSum=0.482;SB=-2.240e+03;VQSLOD=8.13;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,63:63:99:2024,163,0:110 1|0:24,27:51:99:550,0,540:110 1|1:0,48:48:99:1441,111,0:110 12 58867437 rs140632614 G T 829.25 VQSRTrancheSNP99.00to99.90 AC=4;AF=0.667;AN=6;BaseQRankSum=1.41;DB;DP=144;Dels=0.00;FS=68.61;HaplotypeScore=0.867;MLEAC=4;MLEAF=0.667;MQ=35.15;MQ0=16;MQRankSum=-7.440e+00;QD=5.76;ReadPosRankSum=-2.450e-01;SB=-1.011e+00;VQSLOD=-1.649e+01;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:34,24:58:99:291,0,1100:44 0|1:42,8:50:61:61,0,1319:44 1|1:1,35:36:45:519,45,0:44 12 68921960 . TATTTTC T 803.22 VQSRTrancheINDEL99.90to100.00 AC=3;AF=0.500;AN=6;BaseQRankSum=9.86;DP=270;FS=190.60;HaplotypeScore=223.07;MLEAC=3;MLEAF=0.500;MQ=54.84;MQ0=1;MQRankSum=-4.552e+00;QD=2.97;ReadPosRankSum=-6.674e+00;SB=-1.330e-03;VQSLOD=-1.777e+01;culprit=FS GT:AD:DP:GQ:PL:TP 0/1:69,22:95:99:394,0,4974:101 0/1:87,0:86:99:355,0,5072:101 0/1:83,0:84:99:102,0,5546:101 12 79238948 rs10778234 C T 3719.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=8.19;DB;DP=241;Dels=0.00;FS=7.07;HaplotypeScore=0.245;MLEAC=3;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=-3.810e-01;QD=15.43;ReadPosRankSum=0.579;SB=-1.864e+03;VQSLOD=7.81;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0/1:42,35:77:99:1049,0,1213:127 0/1:37,32:69:99:988,0,957:127 0/1:42,53:95:99:1682,0,1062:127 12 90856710 rs825945 T C 1096.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-6.342e+00;DB;DP=193;Dels=0.00;FS=2.16;HaplotypeScore=0.00;MLEAC=2;MLEAF=0.333;MQ=59.64;MQ0=0;MQRankSum=2.07;QD=9.70;ReadPosRankSum=-1.697e+00;SB=-5.710e+02;VQSLOD=7.31;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|0:80,0:80:99:0,232,3042:127 0|1:30,21:51:99:511,0,921:127 0|1:36,26:62:99:624,0,1085:127 12 101460237 rs7965836 C T 3485.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-2.070e+00;DB;DP=247;Dels=0.00;FS=2.89;HaplotypeScore=0.656;MLEAC=3;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-6.550e-01;QD=14.11;ReadPosRankSum=-9.830e-01;SB=-1.581e+03;VQSLOD=8.49;culprit=MQ GT:AD:DP:GQ:PL:TP 0/1:40,43:83:99:1287,0,1179:127 0/1:44,36:80:99:1068,0,1363:127 0/1:43,41:84:99:1130,0,1321:127 12 112830546 rs150699511 C A 487.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-1.014e+00;DB;DP=179;Dels=0.00;FS=0.860;HaplotypeScore=2.34;MLEAC=1;MLEAF=0.167;MQ=59.16;MQ0=0;MQRankSum=1.14;QD=8.86;ReadPosRankSum=0.950;SB=-2.870e+02;VQSLOD=8.11;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:62,0:62:99:0,166,2141:127 0|1:34,21:55:99:522,0,751:127 0|0:62,0:62:99:0,141,1808:127 12 122942070 rs10744217 A G 1812.24 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-3.353e+00;DB;DP=179;Dels=0.00;FS=0.663;HaplotypeScore=1.42;MLEAC=3;MLEAF=0.500;MQ=58.69;MQ0=0;MQRankSum=0.992;QD=15.10;ReadPosRankSum=1.08;SB=-5.860e+02;VQSLOD=8.48;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:35,36:71:99:762,0,1100:92 1|1:0,48:49:93:1095,93,0:92 0|0:59,0:59:99:0,120,1560:92 12 130522866 rs1613499 C T 3975.01 PASS AC=6;AF=1.00;AN=6;DB;DP=130;Dels=0.00;FS=0.00;HaplotypeScore=0.633;MLEAC=6;MLEAF=1.00;MQ=59.11;MQ0=0;QD=30.58;SB=-1.386e+03;VQSLOD=10.23;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,57:57:99:1939,144,0:73 1|1:0,34:34:75:990,75,0:73 1|1:0,39:39:78:1046,78,0:73 13 21520045 rs9509464 A C 5103.01 PASS AC=6;AF=1.00;AN=6;DB;DP=195;Dels=0.00;FS=0.00;HaplotypeScore=1.61;MLEAC=6;MLEAF=1.00;MQ=47.37;MQ0=0;QD=26.17;SB=-2.582e+03;VQSLOD=5.19;culprit=MQ GT:AD:DP:GQ:PL:TP 1|1:0,71:71:99:2106,186,0:98 1|1:0,78:78:99:1856,162,0:98 1|1:0,46:46:99:1141,99,0:98 13 28463938 rs954750 C T 2740.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=3.21;DB;DP=242;Dels=0.00;FS=0.00;HaplotypeScore=4.01;MLEAC=2;MLEAF=0.333;MQ=59.46;MQ0=0;MQRankSum=0.880;QD=16.61;ReadPosRankSum=-6.170e-01;SB=-1.312e+03;VQSLOD=6.77;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:40,43:83:99:1362,0,1242:127 1|0:35,47:82:99:1417,0,1010:127 0|0:76,0:77:99:0,205,2635:127 13 37484693 rs1571317 T C 971.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-2.315e+00;DB;DP=229;Dels=0.00;FS=3.05;HaplotypeScore=0.660;MLEAC=1;MLEAF=0.167;MQ=58.51;MQ0=0;MQRankSum=1.88;QD=12.78;ReadPosRankSum=-3.430e-01;SB=-5.750e+02;VQSLOD=7.31;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:94,0:94:99:0,253,3258:127 0|1:35,41:76:99:1006,0,924:127 0|0:59,0:59:99:0,147,1872:127 13 46407442 rs11147990 G A 2668.24 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=1.23;DB;DP=199;Dels=0.00;FS=0.530;HaplotypeScore=1.80;MLEAC=3;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.023;QD=20.21;ReadPosRankSum=-4.520e-01;SB=-1.651e+03;VQSLOD=9.20;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 0|1:36,33:69:99:994,0,1056:127 0|0:67,0:67:99:0,141,1821:127 1|1:0,63:63:99:1719,135,0:127 13 56456878 rs2997102 C A 9454.01 PASS AC=6;AF=1.00;AN=6;DB;DP=257;Dels=0.00;FS=0.00;HaplotypeScore=0.954;MLEAC=6;MLEAF=1.00;MQ=59.57;MQ0=0;QD=36.79;SB=-4.826e+03;VQSLOD=11.51;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,99:99:99:3692,280,0:127 1|1:0,88:88:99:3239,253,0:127 1|1:0,70:70:99:2523,193,0:127 13 65275154 rs359338 G A 1963.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.73;DB;DP=173;Dels=0.00;FS=3.63;HaplotypeScore=0.948;MLEAC=2;MLEAF=0.333;MQ=59.49;MQ0=0;MQRankSum=-6.760e-01;QD=14.54;ReadPosRankSum=0.399;SB=-1.054e+03;VQSLOD=8.45;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:31,28:59:99:883,0,990:108 1|0:39,37:76:99:1119,0,1112:108 0|0:38,0:38:99:0,108,1390:108 13 74611546 rs73214804 C T 639.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-4.870e-01;DB;DP=164;Dels=0.00;FS=0.00;HaplotypeScore=1.41;MLEAC=1;MLEAF=0.167;MQ=58.95;MQ0=0;MQRankSum=0.902;QD=11.21;ReadPosRankSum=-5.410e-01;SB=-3.000e+02;VQSLOD=8.88;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:53,0:53:99:0,135,1773:110 0|0:53,1:54:99:0,111,1440:110 0|1:24,33:57:99:674,0,388:110 13 83670546 . G A 169.26 VQSRTrancheSNP99.00to99.90 AC=2;AF=0.333;AN=6;BaseQRankSum=5.30;DP=178;Dels=0.00;FS=0.00;HaplotypeScore=36.51;MLEAC=2;MLEAF=0.333;MQ=42.20;MQ0=11;MQRankSum=-6.654e+00;QD=1.38;ReadPosRankSum=-7.610e-01;SB=-1.340e+02;VQSLOD=-2.041e+01;culprit=QD GT:AD:DP:GQ:PL:TP 0|1:37,16:53:99:139,0,523:90 0|0:51,4:55:91:0,91,1393:90 1|0:58,12:70:69:69,0,1214:90 13 92742124 rs2148446 G A 1884.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-2.340e+00;DB;DP=213;Dels=0.00;FS=0.00;HaplotypeScore=0.316;MLEAC=2;MLEAF=0.333;MQ=59.37;MQ0=0;MQRankSum=-2.935e+00;QD=12.99;ReadPosRankSum=-5.790e-01;SB=-9.540e+02;VQSLOD=7.28;culprit=MQRankSum GT:AD:DP:GQ:PL:TP 0|1:38,38:76:99:1130,0,1190:127 0|0:68,0:68:99:0,190,2454:127 1|0:38,31:69:99:793,0,1094:127 13 101976707 rs527328 A T 9240.01 PASS AC=6;AF=1.00;AN=6;DB;DP=259;Dels=0.00;FS=0.00;HaplotypeScore=0.245;MLEAC=6;MLEAF=1.00;MQ=53.28;MQ0=0;QD=35.68;SB=-4.696e+03;VQSLOD=7.52;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:0,92:92:99:3410,262,0:127 1|1:0,88:88:99:3195,247,0:127 1|1:1,78:79:99:2635,202,0:127 13 109990322 rs7328109 T C 7198.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-2.487e+00;DB;DP=245;Dels=0.00;FS=5.89;HaplotypeScore=1.88;MLEAC=5;MLEAF=0.833;MQ=59.60;MQ0=0;MQRankSum=-2.360e-01;QD=29.38;ReadPosRankSum=0.136;SB=-3.593e+03;VQSLOD=8.89;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,79:79:99:2825,220,0:127 1|0:33,54:87:99:1591,0,933:127 1|1:0,79:79:99:2782,214,0:127 14 20313371 rs10137604 A C 2154.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-4.894e+00;DB;DP=255;Dels=0.00;FS=0.00;HaplotypeScore=2.05;MLEAC=2;MLEAF=0.333;MQ=56.32;MQ0=1;MQRankSum=1.61;QD=13.72;ReadPosRankSum=0.126;SB=-1.124e+03;VQSLOD=5.62;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:40,48:88:99:1426,0,1229:127 0|0:98,0:98:99:0,268,3527:127 1|0:43,26:69:99:767,0,1284:127 14 28032147 rs67442200 AT A 9959 PASS AC=6;AF=1.00;AN=6;DB;DP=259;FS=0.00;HaplotypeScore=15.29;MLEAC=6;MLEAF=1.00;MQ=60.66;MQ0=0;QD=38.45;RPA=3,2;RU=T;SB=-4.646e+03;STR;VQSLOD=6.01;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:2,86:91:99:3493,259,0:127 1|1:3,76:79:99:3025,226,0:127 1|1:3,86:89:99:3441,256,0:127 14 38160457 rs2181345 A C 4683.01 PASS AC=6;AF=1.00;AN=6;DB;DP=169;Dels=0.00;FS=0.00;HaplotypeScore=2.54;MLEAC=6;MLEAF=1.00;MQ=59.00;MQ0=0;QD=27.71;SB=-2.390e+03;VQSLOD=9.99;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,56:56:99:1818,141,0:107 1|1:0,58:58:99:1523,123,0:107 1|1:0,53:55:99:1342,108,0:107 14 47568119 rs1952206 T C 3399.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-9.721e+00;DB;DP=230;Dels=0.00;FS=0.483;HaplotypeScore=0.658;MLEAC=3;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-4.790e-01;QD=14.78;ReadPosRankSum=1.26;SB=-1.667e+03;VQSLOD=9.16;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 0/1:41,43:84:99:1239,0,1315:127 0/1:28,43:71:99:1178,0,816:127 0/1:40,35:75:99:982,0,1314:127 14 56951735 rs1189276 G A 6939.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=3.88;DB;DP=235;Dels=0.00;FS=9.37;HaplotypeScore=0.906;MLEAC=5;MLEAF=0.833;MQ=59.52;MQ0=0;MQRankSum=-5.500e-01;QD=29.53;ReadPosRankSum=1.10;SB=-3.438e+03;VQSLOD=8.76;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:1,92:93:99:3558,274,0:127 1|1:0,60:60:99:2120,165,0:127 1|0:40,42:82:99:1261,0,1194:127 14 68051087 rs11628035 G A 4028.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=3.93;DB;DP=236;Dels=0.00;FS=8.18;HaplotypeScore=1.33;MLEAC=3;MLEAF=0.500;MQ=58.83;MQ0=0;MQRankSum=1.83;QD=25.49;ReadPosRankSum=2.59;SB=-1.989e+03;VQSLOD=6.79;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 1|0:38,39:77:99:1265,0,1112:127 1|1:0,81:81:99:2763,214,0:127 0|0:78,0:78:99:0,208,2673:127 14 77813103 rs59474357 G GT 328.58 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-2.653e+00;DB;DP=164;FS=5.22;HaplotypeScore=117.86;MLEAC=5;MLEAF=0.833;MQ=52.18;MQ0=0;MQRankSum=1.26;QD=2.00;RPA=24,25;RU=T;ReadPosRankSum=-1.030e+00;SB=-1.639e+02;STR;VQSLOD=2.16;culprit=QD GT:AD:DP:GQ:PL:TP 1|0:51,1:53:18:105,0,18:6 1|1:58,1:59:13:150,13,0:6 0|1:34,13:52:1:123,6,0:6 14 87263523 rs2542229 A C 8104.01 PASS AC=6;AF=1.00;AN=6;DB;DP=239;Dels=0.00;FS=0.00;HaplotypeScore=0.631;MLEAC=6;MLEAF=1.00;MQ=59.17;MQ0=0;QD=33.91;SB=-4.393e+03;VQSLOD=11.30;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,77:77:99:2810,214,0:127 1|1:0,85:85:99:2877,223,0:127 1|1:0,77:77:99:2417,187,0:127 14 96490389 rs72702859 C G 3394.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-6.529e+00;DB;DP=264;Dels=0.00;FS=2.75;HaplotypeScore=3.13;MLEAC=3;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=-1.258e+00;QD=18.25;ReadPosRankSum=-9.610e-01;SB=-1.966e+03;VQSLOD=6.34;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:34,52:86:99:1358,0,886:127 1|1:0,100:100:99:2036,180,0:127 0|0:78,0:78:99:0,184,2393:127 14 106085773 rs2955055 C T 2115.26 VQSRTrancheSNP99.00to99.90 AC=3;AF=0.500;AN=6;BaseQRankSum=-7.460e-01;DB;DP=172;Dels=0.00;FS=18.42;HaplotypeScore=2.95;MLEAC=3;MLEAF=0.500;MQ=35.68;MQ0=18;MQRankSum=3.25;QD=12.30;ReadPosRankSum=0.100;SB=-5.530e+02;VQSLOD=1.29;culprit=MQ GT:AD:DP:GQ:PL:TP 0/1:32,33:65:99:600,0,554:80 0/1:30,42:72:99:1001,0,400:80 0/1:12,23:35:80:553,0,80:80 15 23743658 rs142070302 T A 1007.26 VQSRTrancheSNP99.90to100.00 AC=3;AF=0.500;AN=6;BaseQRankSum=-3.164e+00;DB;DP=408;Dels=0.00;FS=166.85;HaplotypeScore=53.54;MLEAC=3;MLEAF=0.500;MQ=38.96;MQ0=14;MQRankSum=-6.283e+00;QD=2.47;ReadPosRankSum=2.49;SB=-1.079e-02;VQSLOD=-3.048e+02;culprit=FS GT:AD:DP:GQ:PL:TP 0/1:104,39:143:99:365,0,2802:45 0/1:99,40:139:99:636,0,2335:45 0/1:97,28:126:45:45,0,2324:45 15 32615218 . G GA 82.61 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=0.361;DP=225;FS=0.00;HaplotypeScore=2.49;MLEAC=4;MLEAF=0.667;MQ=5.76;MQ0=211;MQRankSum=-8.760e-01;QD=0.560;RPA=9,10;RU=A;ReadPosRankSum=-1.159e+00;SB=-1.330e-03;STR;VQSLOD=3.74;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:41,19:3:9:88,9,0:5 1|0:62,24:5:44:44,0,77:5 1|0:76,0:1:2:0,3,31:5 15 42065422 rs2925337 A C 5231.01 PASS AC=6;AF=1.00;AN=6;DB;DP=176;Dels=0.00;FS=0.00;HaplotypeScore=0.00;MLEAC=6;MLEAF=1.00;MQ=59.68;MQ0=0;QD=29.72;SB=-3.112e+03;VQSLOD=11.03;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:0,54:54:99:1770,138,0:127 1|1:0,68:68:99:1750,138,0:127 1|1:0,54:54:99:1711,132,0:127 15 53677501 . T G 770.26 VQSRTrancheSNP99.90to100.00 AC=3;AF=0.500;AN=6;BaseQRankSum=-8.969e+00;DP=210;Dels=0.00;FS=347.47;HaplotypeScore=2.09;MLEAC=3;MLEAF=0.500;MQ=58.31;MQ0=0;MQRankSum=0.438;QD=3.67;ReadPosRankSum=-6.409e+00;SB=-5.499e-03;VQSLOD=-3.071e+02;culprit=FS GT:AD:DP:GQ:PL:TP 0/1:59,20:79:94:94,0,1389:94 0/1:41,31:72:99:438,0,721:94 0/1:37,21:59:99:277,0,521:94 15 62088952 rs35033959 A T 3546.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-3.220e+00;DB;DP=241;Dels=0.00;FS=14.29;HaplotypeScore=0.277;MLEAC=3;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=-1.969e+00;QD=14.71;ReadPosRankSum=0.341;SB=-1.970e+03;VQSLOD=6.38;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0/1:45,44:89:99:1265,0,1533:127 0/1:34,38:72:99:1133,0,1137:127 0/1:41,39:80:99:1148,0,1303:127 15 71657506 . A G 140.40 VQSRTrancheSNP99.00to99.90 AC=2;AF=0.333;AN=6;BaseQRankSum=-1.611e+00;DP=133;Dels=0.00;FS=35.59;HaplotypeScore=4.06;MLEAC=2;MLEAF=0.333;MQ=51.29;MQ0=1;MQRankSum=-3.344e+00;QD=1.53;ReadPosRankSum=-3.999e+00;SB=-5.015e+01;VQSLOD=-4.805e+00;culprit=QD GT:AD:DP:GQ:PL:TP 1|0:46,11:57:93:93,0,851:15 1|0:23,12:35:86:86,0,299:15 0|0:33,8:41:15:0,15,503:15 15 83241984 rs11336258 AT A 1748.21 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-1.821e+00;DB;DP=199;FS=5.74;HaplotypeScore=29.94;MLEAC=4;MLEAF=0.667;MQ=59.67;MQ0=0;MQRankSum=1.12;QD=8.78;RPA=15,14;RU=T;ReadPosRankSum=-1.763e+00;SB=-7.830e+02;STR;VQSLOD=3.49;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|1:41,27:72:99:434,0,434:118 0|1:36,26:66:99:470,0,275:118 1|1:11,44:61:99:895,118,0:118 15 92857342 rs12101550 A G 2734.26 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-7.995e+00;DB;DP=226;Dels=0.00;FS=3.76;HaplotypeScore=1.57;MLEAC=3;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=0.761;QD=12.10;ReadPosRankSum=-5.870e-01;SB=-1.469e+03;VQSLOD=9.15;culprit=FS GT:AD:DP:GQ:PL:TP 0/1:45,37:82:99:853,0,1356:127 0/1:29,40:69:99:966,0,852:127 0/1:38,37:75:99:954,0,1085:127 15 100799787 rs4965610 C T 2133.26 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=8.37;DB;DP=230;Dels=0.00;FS=1.04;HaplotypeScore=0.543;MLEAC=3;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=0.169;QD=9.28;ReadPosRankSum=-9.800e-02;SB=-1.328e+03;VQSLOD=7.88;culprit=QD GT:AD:DP:GQ:PL:TP 0/1:40,36:76:99:948,0,701:127 0/1:45,38:83:99:761,0,635:127 0/1:35,36:71:99:463,0,706:127 16 5754758 rs11644707 C T 1012.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.78;DB;DP=161;Dels=0.00;FS=0.00;HaplotypeScore=2.46;MLEAC=2;MLEAF=0.333;MQ=59.71;MQ0=0;MQRankSum=0.699;QD=9.64;ReadPosRankSum=2.62;SB=-5.580e+02;VQSLOD=7.10;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 0|1:31,26:57:99:627,0,943:125 0|0:56,0:56:99:0,126,1597:125 1|0:32,16:48:99:424,0,785:125 16 11397080 rs1019552 T C 2295.44 PASS AC=6;AF=1.00;AN=6;DB;DP=169;Dels=1.000e-02;FS=0.00;HaplotypeScore=8.22;MLEAC=6;MLEAF=1.00;MQ=59.32;MQ0=0;QD=13.58;SB=-2.379e+03;VQSLOD=4.38;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:0,71:71:96:1220,96,0:9 1|1:0,48:48:9:78,9,0:9 1|1:0,48:48:81:1035,81,0:9 16 19633462 rs11371821 C CT 239.23 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-4.097e+00;DB;DP=182;FS=1.34;HaplotypeScore=21.26;MLEAC=4;MLEAF=0.667;MQ=50.55;MQ0=0;MQRankSum=-1.358e+00;QD=1.31;RPA=22,23;RU=T;ReadPosRankSum=-3.963e+00;SB=-9.798e+01;STR;VQSLOD=2.31;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 1|0:61,0:63:45:70,0,45:24 1|1:44,15:58:28:192,28,0:24 0|1:52,0:60:28:28,0,37:24 16 30509723 rs7193693 A G 497.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-4.054e+00;DB;DP=167;Dels=0.00;FS=0.00;HaplotypeScore=1.16;MLEAC=1;MLEAF=0.167;MQ=57.89;MQ0=0;MQRankSum=-5.450e-01;QD=9.38;ReadPosRankSum=0.541;SB=-2.410e+02;VQSLOD=8.43;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:57,0:57:99:0,153,2009:101 0|0:57,0:57:99:0,102,1304:101 0|1:26,27:53:99:532,0,526:101 16 34610294 rs72812776 C T 603.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-1.361e+00;DB;DP=270;Dels=0.00;FS=6.07;HaplotypeScore=3.16;MLEAC=1;MLEAF=0.167;MQ=59.66;MQ0=0;MQRankSum=1.60;QD=7.83;ReadPosRankSum=0.296;SB=-2.820e+02;VQSLOD=3.37;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|0:123,0:123:99:0,343,4443:127 0|0:69,1:70:99:0,184,2397:127 0|1:48,29:77:99:638,0,1483:127 16 55910673 rs17265788 G C 2345.24 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=2.66;DB;DP=208;Dels=0.00;FS=3.16;HaplotypeScore=1.92;MLEAC=3;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-3.330e-01;QD=16.63;ReadPosRankSum=-4.250e-01;SB=-1.468e+03;VQSLOD=8.37;culprit=MQ GT:AD:DP:GQ:PL:TP 0|1:33,33:66:99:769,0,761:122 0|0:67,0:67:99:0,123,1506:122 1|1:0,75:75:99:1621,132,0:122 16 65776985 rs72784548 T C 3527.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=5.44;DB;DP=195;Dels=0.00;FS=1.23;HaplotypeScore=0.879;MLEAC=4;MLEAF=0.667;MQ=58.78;MQ0=0;MQRankSum=1.63;QD=18.09;ReadPosRankSum=1.36;SB=-1.904e+03;VQSLOD=7.68;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 1|1:0,68:68:99:2351,181,0:127 1|0:33,28:61:99:586,0,710:127 1|0:31,35:66:99:590,0,468:127 16 77418810 rs71137811 T TG 7389 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=0.643;DB;DP=244;FS=2.25;HaplotypeScore=114.41;MLEAC=5;MLEAF=0.833;MQ=61.09;MQ0=0;MQRankSum=2.49;QD=30.28;ReadPosRankSum=2.98;SB=-2.597e+03;VQSLOD=2.91;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:8,84:93:99:3558,264,0:127 1|1:8,65:75:99:2723,179,0:127 1|0:42,32:76:99:1108,0,899:127 16 83153777 rs4395063 T C 3143.25 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-1.771e+00;DB;DP=205;Dels=0.00;FS=1.80;HaplotypeScore=1.04;MLEAC=4;MLEAF=0.667;MQ=59.55;MQ0=0;MQRankSum=-1.380e+00;QD=15.33;ReadPosRankSum=0.424;SB=-2.104e+03;VQSLOD=8.82;culprit=FS GT:AD:DP:GQ:PL:TP 0|1:31,31:62:99:867,0,865:127 0|1:45,28:73:99:412,0,801:127 1|1:0,70:70:99:1906,150,0:127 16 88914235 rs12932521 C T 329.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=1.98;DB;DP=114;Dels=0.00;FS=1.93;HaplotypeScore=0.940;MLEAC=1;MLEAF=0.167;MQ=58.60;MQ0=0;MQRankSum=0.854;QD=7.84;ReadPosRankSum=-3.390e-01;SB=-2.970e+02;VQSLOD=8.10;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:43,0:43:99:0,102,1192:39 0|0:29,0:29:39:0,39,468:39 0|1:15,26:42:99:364,0,105:39 17 5764764 rs2309483 C G 4071.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=4.24;DB;DP=154;Dels=0.00;FS=0.00;HaplotypeScore=4.41;MLEAC=5;MLEAF=0.833;MQ=58.88;MQ0=0;MQRankSum=0.456;QD=26.44;ReadPosRankSum=0.385;SB=-1.791e+03;VQSLOD=6.95;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:0,61:62:99:2049,165,0:107 1|0:23,26:49:99:648,0,482:107 1|1:0,43:43:99:1374,108,0:107 17 14096866 . C T 489.26 VQSRTrancheSNP99.00to99.90 AC=3;AF=0.500;AN=6;BaseQRankSum=4.54;DP=181;Dels=0.00;FS=33.90;HaplotypeScore=1.08;MLEAC=3;MLEAF=0.500;MQ=24.52;MQ0=71;MQRankSum=0.353;QD=2.70;ReadPosRankSum=0.385;SB=-1.450e+02;VQSLOD=-6.217e+00;culprit=QD GT:AD:DP:GQ:PL:TP 0/1:48,17:66:99:228,0,822:63 0/1:42,16:58:99:237,0,389:63 0/1:44,13:57:63:63,0,523:63 17 21547285 rs62049731 A C 1322.26 VQSRTrancheSNP99.90to100.00 AC=3;AF=0.500;AN=6;BaseQRankSum=-9.870e-01;DB;DP=569;Dels=0.00;FS=2.32;HaplotypeScore=42.45;MLEAC=3;MLEAF=0.500;MQ=44.59;MQ0=24;MQRankSum=-6.240e+00;QD=2.32;ReadPosRankSum=-5.171e+00;SB=-6.369e+02;VQSLOD=-3.953e+01;culprit=DP GT:AD:DP:GQ:PL:TP 0/1:146,28:174:99:217,0,4187:127 0/1:162,56:218:99:804,0,4298:127 0/1:139,38:177:99:340,0,3842:127 17 33513649 rs3744366 A G 3743.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-3.729e+00;DB;DP=213;Dels=0.00;FS=0.526;HaplotypeScore=2.91;MLEAC=4;MLEAF=0.667;MQ=58.99;MQ0=0;MQRankSum=-1.520e-01;QD=17.57;ReadPosRankSum=0.530;SB=-2.067e+03;VQSLOD=8.02;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:44,40:84:99:1083,0,1341:127 1|1:0,67:67:99:2074,162,0:127 0|1:37,24:62:99:586,0,1015:127 17 44809197 rs116187585 A G 8703.01 PASS AC=6;AF=1.00;AN=6;BaseQRankSum=-5.540e-01;DB;DP=254;Dels=0.00;FS=3.49;HaplotypeScore=4.06;MLEAC=6;MLEAF=1.00;MQ=59.58;MQ0=0;MQRankSum=1.68;QD=34.26;ReadPosRankSum=1.48;SB=-4.228e+03;VQSLOD=6.61;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:1,96:97:99:3470,268,0:127 1|1:0,82:84:99:2846,220,0:127 1|1:0,73:73:99:2387,184,0:127 17 55158811 rs7217371 G A 2849.26 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=8.62;DB;DP=206;Dels=0.00;FS=0.511;HaplotypeScore=1.10;MLEAC=3;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=0.103;QD=13.83;ReadPosRankSum=0.958;SB=-1.448e+03;VQSLOD=9.94;culprit=MQ GT:AD:DP:GQ:PL:TP 0/1:40,31:72:99:982,0,1147:127 0/1:35,40:75:99:1236,0,984:127 0/1:32,27:59:99:670,0,882:127 17 66991216 rs61697543 T C 738.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-4.530e+00;DB;DP=252;Dels=0.00;FS=1.49;HaplotypeScore=1.71;MLEAC=1;MLEAF=0.167;MQ=59.36;MQ0=0;MQRankSum=0.771;QD=10.86;ReadPosRankSum=-7.240e-01;SB=-3.930e+02;VQSLOD=8.89;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:95,0:95:99:0,268,3511:127 0|0:89,0:89:99:0,235,3058:127 0|1:33,35:68:99:773,0,965:127 17 75679403 . TGTG T 1024.22 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=8.62;DP=161;FS=1.69;HaplotypeScore=259.32;MLEAC=2;MLEAF=0.333;MQ=51.57;MQ0=0;MQRankSum=-8.617e+00;QD=9.48;ReadPosRankSum=-4.980e-01;SB=-4.680e+02;VQSLOD=1.76;culprit=QD GT:AD:DP:GQ:PL:TP 1|0:29,19:58:99:711,0,1547:127 1|0:34,11:50:99:361,0,1922:127 0|0:53,0:53:99:0,157,3186:127 18 1629264 rs5025369 A G 86.26 VQSRTrancheSNP99.00to99.90 AC=2;AF=0.333;AN=6;BaseQRankSum=-1.739e+00;DB;DP=149;Dels=0.00;FS=15.36;HaplotypeScore=7.14;MLEAC=2;MLEAF=0.333;MQ=39.72;MQ0=11;MQRankSum=-2.543e+00;QD=0.810;ReadPosRankSum=0.088;SB=-3.380e+01;VQSLOD=-6.205e+00;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|1:51,15:66:50:50,0,1143:49 0|0:37,5:42:81:0,81,941:49 1|0:35,6:41:75:75,0,818:49 18 10010426 rs4797393 T C 4197.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=0.425;DB;DP=210;Dels=0.00;FS=1.13;HaplotypeScore=1.27;MLEAC=4;MLEAF=0.667;MQ=59.43;MQ0=0;MQRankSum=-2.916e+00;QD=19.99;ReadPosRankSum=0.379;SB=-2.001e+03;VQSLOD=7.03;culprit=MQRankSum GT:AD:DP:GQ:PL:TP 1|1:0,65:65:99:2247,181,0:127 1|0:35,39:75:99:1170,0,967:127 1|0:41,29:70:99:780,0,1052:127 18 20025030 rs4800406 A G 1113.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-3.700e+00;DB;DP=230;Dels=0.00;FS=0.00;HaplotypeScore=1.68;MLEAC=1;MLEAF=0.167;MQ=59.56;MQ0=0;MQRankSum=1.64;QD=12.65;ReadPosRankSum=-1.166e+00;SB=-6.160e+02;VQSLOD=8.66;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:78,0:78:99:0,223,2978:127 0|1:46,42:88:99:1148,0,1460:127 0|0:64,0:64:99:0,175,2303:127 18 30361151 rs35024407 T TTG 9768 PASS AC=6;AF=1.00;AN=6;DB;DP=234;FS=0.00;HaplotypeScore=13.10;MLEAC=6;MLEAF=1.00;MQ=60.40;MQ0=2;QD=41.74;RPA=3,4;RU=TG;SB=-4.721e+03;STR;VQSLOD=5.50;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:7,80:86:99:3686,241,0:127 1|1:8,77:85:99:3454,229,0:127 1|1:3,58:61:99:2628,172,0:127 18 41449098 rs2045671 C T 8380.01 PASS AC=6;AF=1.00;AN=6;DB;DP=237;Dels=0.00;FS=0.00;HaplotypeScore=1.35;MLEAC=6;MLEAF=1.00;MQ=59.65;MQ0=0;QD=35.36;SB=-4.462e+03;VQSLOD=11.65;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,76:76:99:2756,214,0:127 1|1:0,75:75:99:2635,202,0:127 1|1:0,86:86:99:2989,229,0:127 18 50973169 rs11661305 A G 5320.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=2.75;DB;DP=196;Dels=0.00;FS=2.57;HaplotypeScore=1.13;MLEAC=5;MLEAF=0.833;MQ=57.73;MQ0=0;MQRankSum=0.246;QD=27.14;ReadPosRankSum=0.186;SB=-2.411e+03;VQSLOD=7.50;culprit=MQ GT:AD:DP:GQ:PL:TP 1|1:0,74:74:99:2621,202,0:127 1|0:30,37:67:99:1009,0,842:127 1|1:0,55:55:99:1690,132,0:127 18 59836086 . A AT 575.46 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-1.815e+00;DP=231;FS=20.46;HaplotypeScore=140.20;MLEAC=3;MLEAF=0.500;MQ=56.52;MQ0=0;MQRankSum=1.20;QD=2.49;RPA=20,21;RU=T;ReadPosRankSum=-1.968e+00;SB=-2.575e+02;STR;VQSLOD=-3.166e-01;culprit=FS GT:AD:DP:GQ:PL:TP 0/1:52,29:86:11:309,0,11:9 0/1:72,2:82:63:109,0,63:9 0/1:31,24:63:15:205,0,15:9 18 67950442 rs62091919 T G 1779.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-2.517e+00;DB;DP=195;Dels=0.00;FS=0.562;HaplotypeScore=1.55;MLEAC=2;MLEAF=0.333;MQ=59.26;MQ0=0;MQRankSum=6.000e-03;QD=12.89;ReadPosRankSum=-2.680e-01;SB=-9.170e+02;VQSLOD=9.63;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 0|1:40,32:72:99:967,0,1318:127 0|0:55,2:57:99:0,141,1865:127 1|0:36,30:66:99:851,0,1042:127 18 75204349 rs9948476 C T 646.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=1.97;DB;DP=185;Dels=0.00;FS=0.817;HaplotypeScore=1.40;MLEAC=1;MLEAF=0.167;MQ=59.35;MQ0=0;MQRankSum=0.276;QD=10.95;ReadPosRankSum=-1.580e-01;SB=-3.210e+02;VQSLOD=9.37;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:65,0:66:99:0,168,2026:127 0|0:60,0:60:99:0,147,1768:127 0|1:34,25:59:99:681,0,893:127 19 3739001 rs56138006 C T 976.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=4.63;DB;DP=118;Dels=0.00;FS=3.68;HaplotypeScore=1.44;MLEAC=2;MLEAF=0.333;MQ=58.66;MQ0=0;MQRankSum=0.753;QD=11.22;ReadPosRankSum=1.11;SB=-6.380e+02;VQSLOD=7.45;culprit=QD GT:AD:DP:GQ:PL:TP 0|1:30,22:52:99:612,0,559:45 0|0:31,0:31:45:0,45,527:45 1|0:12,23:35:93:403,0,93:45 19 11730690 rs4804613 C T 2578.26 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=5.06;DB;DP=197;Dels=0.00;FS=0.529;HaplotypeScore=0.00;MLEAC=3;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.416;QD=13.09;ReadPosRankSum=-5.540e-01;SB=-1.389e+03;VQSLOD=9.39;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0/1:21,26:47:99:586,0,623:127 0/1:42,45:87:99:1192,0,1055:127 0/1:32,30:63:99:839,0,932:127 19 20782710 rs10413568 T C 6304.01 PASS AC=6;AF=1.00;AN=6;DB;DP=203;Dels=0.00;FS=0.00;HaplotypeScore=0.692;MLEAC=6;MLEAF=1.00;MQ=59.56;MQ0=0;QD=31.05;SB=-2.367e+03;VQSLOD=10.77;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,74:74:99:2375,214,0:127 1|1:0,80:80:99:2480,217,0:127 1|1:0,49:49:99:1449,129,0:127 19 28150587 rs4404191 A G 7419.01 PASS AC=6;AF=1.00;AN=6;DB;DP=209;Dels=0.00;FS=0.00;HaplotypeScore=0.245;MLEAC=6;MLEAF=1.00;MQ=59.61;MQ0=0;QD=35.50;SB=-3.717e+03;VQSLOD=11.99;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|1:0,70:70:99:2584,202,0:127 1|1:0,74:74:99:2509,193,0:127 1|1:0,65:65:99:2326,181,0:127 19 37226152 rs3108217 G C 2076.25 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=0.215;DB;DP=145;Dels=0.00;FS=2.16;HaplotypeScore=0.587;MLEAC=4;MLEAF=0.667;MQ=58.59;MQ0=0;MQRankSum=1.16;QD=14.32;ReadPosRankSum=-7.250e-01;SB=-1.027e+03;VQSLOD=7.49;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:25,30:55:99:789,0,709:63 1|1:0,29:29:63:772,63,0:63 0|1:35,25:61:99:557,0,789:63 19 47012249 rs60424854 ATTTTT A 1121.22 VQSRTrancheINDEL99.00to99.90 AC=2;AF=0.333;AN=6;BaseQRankSum=-1.922e+00;DB;DP=144;FS=61.85;HaplotypeScore=338.74;MLEAC=2;MLEAF=0.333;MQ=44.50;MQ0=1;MQRankSum=-2.345e+00;QD=10.29;RPA=16,11;RU=T;ReadPosRankSum=5.64;SB=-1.090e+02;STR;VQSLOD=-2.399e+00;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 1|0:30,9:43:99:371,0,961:89 1|0:44,15:63:99:798,0,1293:89 0|0:32,0:33:89:0,89,1424:89 19 54644879 rs36636 G A 1790.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=2.51;DB;DP=187;Dels=0.00;FS=4.41;HaplotypeScore=1.50;MLEAC=2;MLEAF=0.333;MQ=59.51;MQ0=0;MQRankSum=-1.266e+00;QD=13.88;ReadPosRankSum=-1.226e+00;SB=-1.081e+03;VQSLOD=7.80;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:30,27:57:99:811,0,726:127 1|0:31,41:72:99:1018,0,730:127 0|0:58,0:58:99:0,144,1815:127 20 3199373 rs2422861 G A 896.26 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=0.452;DB;DP=135;Dels=0.00;FS=0.664;HaplotypeScore=2.84;MLEAC=3;MLEAF=0.500;MQ=58.47;MQ0=0;MQRankSum=-2.170e-01;QD=6.64;ReadPosRankSum=0.111;SB=-6.080e+02;VQSLOD=7.71;culprit=QD GT:AD:DP:GQ:PL:TP 0/1:32,24:56:99:472,0,640:127 0/1:25,15:40:99:229,0,603:127 0/1:20,19:39:99:234,0,379:127 20 12166868 rs7272217 C T 926.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-3.444e+00;DB;DP=200;Dels=0.00;FS=2.63;HaplotypeScore=0.841;MLEAC=1;MLEAF=0.167;MQ=58.94;MQ0=0;MQRankSum=-1.362e+00;QD=13.23;ReadPosRankSum=-1.055e+00;SB=-4.040e+02;VQSLOD=7.62;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:68,0:68:99:0,190,2486:127 0|0:62,0:62:99:0,169,2218:127 0|1:33,37:70:99:961,0,870:127 20 21523349 rs73127889 A G 2286.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-6.469e+00;DB;DP=253;Dels=0.00;FS=3.73;HaplotypeScore=1.54;MLEAC=2;MLEAF=0.333;MQ=59.31;MQ0=0;MQRankSum=0.821;QD=13.69;ReadPosRankSum=1.51;SB=-8.640e+02;VQSLOD=7.84;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 0|1:44,48:92:99:1319,0,1356:127 0|0:86,0:86:99:0,235,2994:127 1|0:37,38:75:99:1006,0,1111:127 20 29566945 rs6119037 C G 1427.26 VQSRTrancheSNP99.00to99.90 AC=2;AF=0.333;AN=6;BaseQRankSum=-3.826e+00;DB;DP=271;Dels=0.00;FS=1.15;HaplotypeScore=2.76;MLEAC=2;MLEAF=0.333;MQ=47.42;MQ0=21;MQRankSum=2.42;QD=8.06;ReadPosRankSum=0.363;SB=-7.560e+02;VQSLOD=1.79;culprit=MQ GT:AD:DP:GQ:PL:TP 1|0:59,32:91:99:782,0,1210:127 1|0:55,31:86:99:684,0,1422:127 0|0:94,0:94:99:0,208,2592:127 20 41560394 rs761027 A G 5634.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-4.444e+00;DB;DP=222;Dels=0.00;FS=0.829;HaplotypeScore=1.14;MLEAC=5;MLEAF=0.833;MQ=59.60;MQ0=0;MQRankSum=0.392;QD=25.38;ReadPosRankSum=-6.400e-02;SB=-3.048e+03;VQSLOD=10.04;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,72:72:99:2228,187,0:127 1|1:0,82:82:99:2435,211,0:127 1|0:25,43:68:99:971,0,567:127 20 51353834 rs241795 G A 6115.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=7.91;DB;DP=268;Dels=0.00;FS=0.00;HaplotypeScore=0.245;MLEAC=4;MLEAF=0.667;MQ=59.38;MQ0=0;MQRankSum=-5.180e-01;QD=22.82;ReadPosRankSum=-2.530e-01;SB=-3.328e+03;VQSLOD=8.40;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:46,54:100:99:1663,0,1247:127 1|1:0,91:91:99:3189,247,0:127 0|1:36,41:77:99:1263,0,901:127 20 59978756 rs1892320 T C 3967.01 PASS AC=4;AF=0.667;AN=6;BaseQRankSum=-2.562e+00;DB;DP=206;Dels=0.00;FS=14.25;HaplotypeScore=1.38;MLEAC=4;MLEAF=0.667;MQ=59.89;MQ0=0;MQRankSum=-2.890e-01;QD=19.26;ReadPosRankSum=0.221;SB=-2.292e+03;VQSLOD=7.62;culprit=MQ GT:AD:DP:GQ:PL:TP 1|1:0,72:72:99:2337,181,0:127 1|0:38,29:67:99:743,0,1180:127 1|0:31,36:67:99:887,0,873:127 21 10750991 . C T 602.26 VQSRTrancheSNP99.90to100.00 AC=2;AF=0.333;AN=6;BaseQRankSum=10.10;DP=735;DS;Dels=0.00;FS=27.02;HaplotypeScore=107.27;MLEAC=2;MLEAF=0.333;MQ=44.40;MQ0=2;MQRankSum=-1.456e+01;QD=1.24;ReadPosRankSum=0.063;SB=-8.430e+02;VQSLOD=-1.009e+02;culprit=DP GT:AD:DP:GQ:PL:TP 1|0:164,78:243:99:357,0,5193:103 1|0:187,55:242:99:284,0,5252:103 0|0:199,50:250:99:0,103,5864:103 21 18433036 rs969905 A G 781.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-6.610e+00;DB;DP=229;Dels=0.00;FS=2.23;HaplotypeScore=1.29;MLEAC=1;MLEAF=0.167;MQ=59.55;MQ0=0;MQRankSum=0.300;QD=10.15;ReadPosRankSum=-3.840e-01;SB=-4.990e+02;VQSLOD=9.58;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:62,0:63:99:0,181,2380:127 0|0:89,0:89:99:0,244,3177:127 0|1:39,38:77:99:816,0,1256:127 21 25702950 rs2260875 C G 3462.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=0.156;DB;DP=237;Dels=0.00;FS=2.90;HaplotypeScore=1.54;MLEAC=3;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=0.386;QD=14.61;ReadPosRankSum=-1.455e+00;SB=-1.683e+03;VQSLOD=8.05;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 0/1:37,40:77:99:1282,0,1101:127 0/1:43,36:79:99:1114,0,1317:127 0/1:45,36:81:99:1066,0,1329:127 21 34546711 rs11701692 T C 1030.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-1.884e+00;DB;DP=152;Dels=0.00;FS=8.32;HaplotypeScore=1.93;MLEAC=2;MLEAF=0.333;MQ=57.61;MQ0=0;MQRankSum=-2.910e-01;QD=10.51;ReadPosRankSum=0.258;SB=-4.600e+02;VQSLOD=6.46;culprit=FS GT:AD:DP:GQ:PL:TP 1|0:35,25:61:99:574,0,1137:127 1|0:19,18:37:99:495,0,498:127 0|0:54,0:54:99:0,141,1811:127 21 42833227 rs460904 T C 3179.23 PASS AC=6;AF=1.00;AN=6;DB;DP=155;Dels=0.00;FS=0.00;HaplotypeScore=2.46;MLEAC=6;MLEAF=1.00;MQ=58.18;MQ0=0;QD=20.51;SB=-2.173e+03;VQSLOD=7.70;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,60:60:90:1085,90,0:74 1|1:0,54:54:96:1172,96,0:74 1|1:0,41:41:75:960,75,0:74 22 17351507 rs5748687 G A 4244.01 VQSRTrancheSNP99.00to99.90 AC=5;AF=0.833;AN=6;BaseQRankSum=-2.240e-01;DB;DP=261;Dels=0.00;FS=0.710;HaplotypeScore=1.72;MLEAC=5;MLEAF=0.833;MQ=28.84;MQ0=57;MQRankSum=-7.852e+00;QD=16.26;ReadPosRankSum=-1.243e+00;SB=-2.174e+03;VQSLOD=-1.710e+00;culprit=MQ GT:AD:DP:GQ:PL:TP 1|1:0,92:92:99:1529,141,0:127 1|0:34,49:83:99:727,0,1065:127 1|1:0,86:86:99:1988,180,0:127 22 24416101 rs66532277 C CTT 458.98 VQSRTrancheINDEL99.00to99.90 AC=3;AF=0.500;AN=6;BaseQRankSum=-4.190e+00;DB;DP=251;FS=68.55;HaplotypeScore=55.31;MLEAC=3;MLEAF=0.500;MQ=51.85;MQ0=3;MQRankSum=2.42;QD=1.83;RPA=23,25;RU=T;ReadPosRankSum=2.88;SB=-3.571e+01;STR;VQSLOD=-2.028e+00;culprit=QD GT:AD:DP:GQ:PL:TP 0/1:68,20:91:65:207,0,65:3 0/1:84,0:83:0:184,0,0:3 0/1:72,0:72:83:114,0,83:3 22 34204930 rs13053313 T C 435.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-2.517e+00;DB;DP=82;Dels=0.00;FS=5.84;HaplotypeScore=0.533;MLEAC=1;MLEAF=0.167;MQ=58.65;MQ0=0;MQRankSum=1.12;QD=12.80;ReadPosRankSum=-1.270e+00;SB=-1.170e+02;VQSLOD=6.44;culprit=DP GT:AD:DP:GQ:PL:TP 0|0:12,0:12:27:0,27,360:27 0|1:16,18:34:99:470,0,403:27 0|0:36,0:36:93:0,93,1230:27 22 43356130 rs6519353 A C 3526.01 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=0.809;DB;DP=228;Dels=0.00;FS=6.34;HaplotypeScore=1.63;MLEAC=3;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=-1.460e-01;QD=22.46;ReadPosRankSum=2.03;SB=-1.954e+03;VQSLOD=8.50;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 1|0:40,41:81:99:1020,0,1222:127 1|1:0,76:76:99:2506,196,0:127 0|0:71,0:71:99:0,165,2091:127 22 50309915 rs9616205 A T 1712.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-9.360e-01;DB;DP=162;Dels=0.00;FS=2.86;HaplotypeScore=2.15;MLEAC=2;MLEAF=0.333;MQ=56.21;MQ0=5;MQRankSum=0.892;QD=13.92;ReadPosRankSum=-1.040e+00;SB=-9.940e+02;VQSLOD=6.28;culprit=MQ GT:AD:DP:GQ:PL:TP 0|1:39,33:72:99:777,0,994:78 0|0:39,0:39:78:0,78,1010:78 1|0:16,35:51:99:974,0,257:78 X 4712340 rs5915814 C A 2233.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=8.78;DB;DP=176;Dels=0.00;FS=0.00;HaplotypeScore=0.443;MLEAC=2;MLEAF=0.333;MQ=59.50;MQ0=0;MQRankSum=-1.782e+00;QD=15.73;ReadPosRankSum=0.359;SB=-1.240e+03;VQSLOD=8.39;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|1:32,37:69:99:1114,0,859:81 0|0:34,0:34:81:0,81,948:81 1|0:32,41:73:99:1158,0,575:81 X 23948720 rs35152285 C CA 535.35 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-3.538e+00;DB;DP=148;FS=0.00;HaplotypeScore=24.32;MLEAC=3;MLEAF=0.500;MQ=53.02;MQ0=0;MQRankSum=0.234;QD=3.62;RPA=16,17;RU=A;ReadPosRankSum=-1.638e+00;SB=-2.841e+02;STR;VQSLOD=3.02;culprit=FS GT:AD:DP:GQ:PL:TP 0/1:37,27:68:62:391,0,62:13 0/1:16,8:25:13:102,0,13:13 0/1:47,4:53:90:90,0,142:13 X 42192093 rs58959554 T C 1058.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-5.464e+00;DB;DP=190;Dels=0.00;FS=6.81;HaplotypeScore=1.88;MLEAC=1;MLEAF=0.167;MQ=59.41;MQ0=0;MQRankSum=-2.120e-01;QD=15.34;ReadPosRankSum=-1.730e-01;SB=-3.970e+02;VQSLOD=8.06;culprit=FS GT:AD:DP:GQ:PL:TP 0|0:70,1:71:99:0,182,2683:127 0|0:50,0:50:99:0,138,1794:127 0|1:31,38:69:99:1093,0,947:127 X 66290558 rs1606094 C T 2602.24 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=2.17;DB;DP=213;Dels=0.00;FS=13.13;HaplotypeScore=0.00;MLEAC=3;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=1.34;QD=18.86;ReadPosRankSum=2.27;SB=-1.122e+03;VQSLOD=6.00;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 1|0:54,47:101:99:1381,0,1762:99 1|1:0,37:37:99:1266,99,0:99 0|0:75,0:75:99:0,205,2705:99 X 84165195 rs5923187 C A 1009.24 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-2.103e+00;DB;DP=194;Dels=0.00;FS=3.07;HaplotypeScore=2.82;MLEAC=1;MLEAF=0.167;MQ=59.31;MQ0=0;MQRankSum=-6.750e-01;QD=12.01;ReadPosRankSum=-1.463e+00;SB=-5.890e+02;VQSLOD=8.24;culprit=HaplotypeScore GT:AD:DP:GQ:PL:TP 0|0:79,1:80:99:0,223,2856:60 0|0:30,0:30:60:0,60,764:60 0|1:40,44:84:99:1044,0,1007:60 X 95868251 . G A 108.36 VQSRTrancheSNP99.00to99.90 AC=2;AF=0.333;AN=6;BaseQRankSum=1.44;DP=90;Dels=0.00;FS=4.21;HaplotypeScore=4.94;MLEAC=2;MLEAF=0.333;MQ=44.60;MQ0=8;MQRankSum=-2.939e+00;QD=1.55;ReadPosRankSum=2.87;SB=-7.411e+01;VQSLOD=-3.242e+00;culprit=QD GT:AD:DP:GQ:PL:TP 0|1:29,9:38:99:126,0,251:23 0|0:20,0:20:24:0,24,266:23 1|0:27,5:32:21:21,0,97:23 X 116855730 rs980389 A G 2366.24 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-3.939e+00;DB;DP=173;Dels=0.00;FS=3.51;HaplotypeScore=0.908;MLEAC=3;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.653;QD=21.51;ReadPosRankSum=0.730;SB=-1.218e+03;VQSLOD=7.96;culprit=MQ GT:AD:DP:GQ:PL:TP 1|0:37,33:70:99:965,0,1249:114 1|1:0,40:40:99:1446,114,0:114 0|0:63,0:63:99:0,175,2284:114 X 135282092 rs5974586 G C 2193.26 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=4.26;DB;DP=203;Dels=0.00;FS=0.540;HaplotypeScore=0.659;MLEAC=2;MLEAF=0.333;MQ=59.47;MQ0=0;MQRankSum=1.00;QD=13.46;ReadPosRankSum=1.34;SB=-1.069e+03;VQSLOD=9.09;culprit=ReadPosRankSum GT:AD:DP:GQ:PL:TP 0|1:47,33:80:99:1026,0,1466:116 0|0:40,0:40:99:0,117,1486:116 1|0:43,40:83:99:1206,0,1311:116 X 150239197 rs6627349 T C 4677.01 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=0.731;DB;DP=179;Dels=0.00;FS=0.00;HaplotypeScore=1.61;MLEAC=5;MLEAF=0.833;MQ=59.69;MQ0=0;MQRankSum=0.676;QD=26.13;ReadPosRankSum=0.494;SB=-2.442e+03;VQSLOD=10.55;culprit=FS GT:AD:DP:GQ:PL:TP 1|1:0,66:66:99:2387,190,0:99 1|1:0,40:40:99:1243,99,0:99 1|0:36,37:73:99:1047,0,1039:99 Y 13265732 . C T 356.72 VQSRTrancheSNP99.00to99.90 AC=2;AF=0.333;AN=6;BaseQRankSum=2.82;DP=142;Dels=0.00;FS=7.94;HaplotypeScore=19.82;MLEAC=2;MLEAF=0.333;MQ=38.22;MQ0=11;MQRankSum=-2.145e+00;QD=5.10;ReadPosRankSum=1.49;SB=-1.466e+00;VQSLOD=-1.443e+01;culprit=MQ GT:AD:DP:GQ:PL:TP 0|1:35,15:50:99:327,0,624:5 0|0:65,7:72:4:0,4,1831:5 1|0:15,5:20:67:67,0,227:5 Y 59024923 . A T 1977.26 VQSRTrancheSNP99.90to100.00 AC=3;AF=0.500;AN=6;BaseQRankSum=1.84;DP=745;DS;Dels=0.00;FS=0.367;HaplotypeScore=8.30;MLEAC=3;MLEAF=0.500;MQ=43.53;MQ0=19;MQRankSum=2.50;QD=2.65;ReadPosRankSum=0.098;SB=-9.720e+02;VQSLOD=-3.676e+01;culprit=DP GT:AD:DP:GQ:PL:TP 0/1:208,42:250:99:730,0,6428:127 0/1:210,35:245:99:588,0,6218:127 0/1:208,42:250:99:698,0,6060:127 GL000214.1 115144 . C T 102.07 VQSRTrancheSNP99.00to99.90 AC=2;AF=0.333;AN=6;BaseQRankSum=0.854;DP=103;Dels=0.00;FS=14.19;HaplotypeScore=14.95;MLEAC=2;MLEAF=0.333;MQ=38.45;MQ0=1;MQRankSum=-2.314e+00;QD=1.05;ReadPosRankSum=1.48;SB=-6.153e+01;VQSLOD=-1.476e+01;culprit=QD GT:AD:DP:GQ:PL:TP 0|0:6,0:6:3:0,3,22:4 0|1:9,11:20:16:81,0,16:4 0|1:63,14:77:58:58,0,908:4 GL000215.1 142616 . T C 976.25 VQSRTrancheSNP99.00to99.90 AC=6;AF=1.00;AN=6;DP=80;Dels=0.00;FS=0.00;HaplotypeScore=0.00;MLEAC=6;MLEAF=1.00;MQ=21.04;MQ0=42;QD=12.20;SB=-8.001e+01;VQSLOD=-4.104e-01;culprit=MQ GT:AD:DP:GQ:PL:TP 1|1:0,33:33:42:516,42,0:19 1|1:0,21:21:24:272,24,0:19 1|1:0,26:26:21:226,21,0:19 GL000212.1 28454 . T C 2248.99 VQSRTrancheSNP99.00to99.90 AC=4;AF=1.00;AN=4;BaseQRankSum=1.69;DP=94;Dels=0.00;FS=3.27;HaplotypeScore=0.962;MLEAC=4;MLEAF=1.00;MQ=36.99;MQ0=7;MQRankSum=-4.280e-01;QD=24.18;ReadPosRankSum=-1.284e+00;SB=-1.053e+03;VQSLOD=1.24;culprit=MQ GT:AD:DP:GQ:PL:TP 1|1:0,29:29:63:755,63,0:63 ./. 1|1:1,63:64:99:1530,135,0:63