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##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> ##FILTER=<ID=LowQual,Description="Low quality"> ##FILTER=<ID=VQSRTrancheINDEL95.00to96.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: 0.9364 <= x < 1.0415"> ##FILTER=<ID=VQSRTrancheINDEL96.00to97.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: 0.8135 <= x < 0.9364"> ##FILTER=<ID=VQSRTrancheINDEL97.00to99.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: 0.323 <= x < 0.8135"> ##FILTER=<ID=VQSRTrancheINDEL99.00to99.50,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -0.1071 <= x < 0.323"> ##FILTER=<ID=VQSRTrancheINDEL99.50to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -1.845 <= x < -0.1071"> ##FILTER=<ID=VQSRTrancheINDEL99.90to99.95,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -3.2441 <= x < -1.845"> ##FILTER=<ID=VQSRTrancheINDEL99.95to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -57172.0693"> ##FILTER=<ID=VQSRTrancheINDEL99.95to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -57172.0693 <= x < -3.2441"> ##FILTER=<ID=VQSRTrancheSNP99.50to99.60,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -0.751 <= x < -0.6681"> ##FILTER=<ID=VQSRTrancheSNP99.60to99.80,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -1.0839 <= x < -0.751"> ##FILTER=<ID=VQSRTrancheSNP99.80to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -1.7082 <= x < -1.0839"> ##FILTER=<ID=VQSRTrancheSNP99.90to99.95,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -3.0342 <= x < -1.7082"> ##FILTER=<ID=VQSRTrancheSNP99.95to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -40235.9641"> ##FILTER=<ID=VQSRTrancheSNP99.95to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -40235.9641 <= x < -3.0342"> ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)"> ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> ##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive) ##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive) ##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive) ##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive) ##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive) ##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive) ##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive) ##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive) ##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive) ##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive) ##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive) ##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive) ##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive) ##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive) ##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive) ##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive) ##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive) ##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive) ##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive) ##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive) ##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive) ##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive) ##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive) ##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive) ##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive) ##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive) ##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive) ##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive) ##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive) ##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive) ##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive) ##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive) ##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive) ##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive) ##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive) ##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive) ##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive) ##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive) ##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive) ##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive) ##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive) ##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive) ##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive) ##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive) ##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive) ##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive) ##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive) ##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive) ##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive) ##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive) ##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive) ##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive) ##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive) ##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive) ##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive) ##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive) ##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive) ##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive) ##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive) ##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive) ##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive) ##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive) ##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive) ##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive) ##GVCFBlock99-2147483647=minGQ=99(inclusive),maxGQ=2147483647(exclusive) ##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=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> ##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=END,Number=1,Type=Integer,Description="Stop position of the interval"> ##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> ##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=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> ##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants"> ##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants"> ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> ##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality"> ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> ##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> ##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds 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"> ##contig=<ID=chr1,length=248956422> ##contig=<ID=chr2,length=242193529> ##contig=<ID=chr3,length=198295559> ##contig=<ID=chr4,length=190214555> ##contig=<ID=chr5,length=181538259> ##contig=<ID=chr6,length=170805979> ##contig=<ID=chr7,length=159345973> ##contig=<ID=chr8,length=145138636> 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##contig=<ID=HLA-DQA1*01:07,length=5959> ##contig=<ID=HLA-DQA1*01:10,length=5790> ##contig=<ID=HLA-DQA1*01:11,length=5926> ##contig=<ID=HLA-DQA1*02:01,length=6403> ##contig=<ID=HLA-DQA1*03:01:01,length=6437> ##contig=<ID=HLA-DQA1*03:02,length=6437> ##contig=<ID=HLA-DQA1*03:03:01,length=6437> ##contig=<ID=HLA-DQA1*04:01:02:01,length=5853> ##contig=<ID=HLA-DQA1*04:01:02:02,length=5666> ##contig=<ID=HLA-DQA1*04:02,length=6210> ##contig=<ID=HLA-DQA1*05:01:01:01,length=5806> ##contig=<ID=HLA-DQA1*05:01:01:02,length=6529> ##contig=<ID=HLA-DQA1*05:03,length=6121> ##contig=<ID=HLA-DQA1*05:05:01:01,length=6593> ##contig=<ID=HLA-DQA1*05:05:01:02,length=6597> ##contig=<ID=HLA-DQA1*05:05:01:03,length=6393> ##contig=<ID=HLA-DQA1*05:11,length=6589> ##contig=<ID=HLA-DQA1*06:01:01,length=5878> ##contig=<ID=HLA-DQB1*02:01:01,length=7480> ##contig=<ID=HLA-DQB1*02:02:01,length=7471> ##contig=<ID=HLA-DQB1*03:01:01:01,length=7231> ##contig=<ID=HLA-DQB1*03:01:01:02,length=7230> ##contig=<ID=HLA-DQB1*03:01:01:03,length=7231> ##contig=<ID=HLA-DQB1*03:02:01,length=7126> ##contig=<ID=HLA-DQB1*03:03:02:01,length=7126> ##contig=<ID=HLA-DQB1*03:03:02:02,length=7126> ##contig=<ID=HLA-DQB1*03:03:02:03,length=6800> ##contig=<ID=HLA-DQB1*03:05:01,length=6934> ##contig=<ID=HLA-DQB1*05:01:01:01,length=7090> ##contig=<ID=HLA-DQB1*05:01:01:02,length=7090> ##contig=<ID=HLA-DQB1*05:03:01:01,length=7089> ##contig=<ID=HLA-DQB1*05:03:01:02,length=7089> ##contig=<ID=HLA-DQB1*06:01:01,length=7111> ##contig=<ID=HLA-DQB1*06:02:01,length=7102> ##contig=<ID=HLA-DQB1*06:03:01,length=7103> ##contig=<ID=HLA-DQB1*06:09:01,length=7102> ##contig=<ID=HLA-DRB1*01:01:01,length=10741> ##contig=<ID=HLA-DRB1*01:02:01,length=11229> ##contig=<ID=HLA-DRB1*03:01:01:01,length=13908> ##contig=<ID=HLA-DRB1*03:01:01:02,length=13426> ##contig=<ID=HLA-DRB1*04:03:01,length=15246> ##contig=<ID=HLA-DRB1*07:01:01:01,length=16110> ##contig=<ID=HLA-DRB1*07:01:01:02,length=16120> ##contig=<ID=HLA-DRB1*08:03:02,length=13562> ##contig=<ID=HLA-DRB1*09:21,length=16039> ##contig=<ID=HLA-DRB1*10:01:01,length=13501> ##contig=<ID=HLA-DRB1*11:01:01,length=13921> ##contig=<ID=HLA-DRB1*11:01:02,length=13931> ##contig=<ID=HLA-DRB1*11:04:01,length=13919> ##contig=<ID=HLA-DRB1*12:01:01,length=13404> ##contig=<ID=HLA-DRB1*12:17,length=11260> ##contig=<ID=HLA-DRB1*13:01:01,length=13935> ##contig=<ID=HLA-DRB1*13:02:01,length=13941> ##contig=<ID=HLA-DRB1*14:05:01,length=13933> ##contig=<ID=HLA-DRB1*14:54:01,length=13936> ##contig=<ID=HLA-DRB1*15:01:01:01,length=11080> ##contig=<ID=HLA-DRB1*15:01:01:02,length=11571> ##contig=<ID=HLA-DRB1*15:01:01:03,length=11056> ##contig=<ID=HLA-DRB1*15:01:01:04,length=11056> ##contig=<ID=HLA-DRB1*15:02:01,length=10313> ##contig=<ID=HLA-DRB1*15:03:01:01,length=11567> ##contig=<ID=HLA-DRB1*15:03:01:02,length=11569> ##contig=<ID=HLA-DRB1*16:02:01,length=11005> ##contig=<ID=NC_007605,length=171823> ##reference=file://reference.fa #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878_18_99 chr1 13613 . T A 39.88 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.29;MQRankSum=0.727;QD=9.97;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=-2.146e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:1,3:4:16:68,0,16 chr1 13813 . T G 90.28 PASS AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.29;QD=30.09;SOR=2.833;VQSLOD=1.38;culprit=SOR GT:AD:DP:GQ:PGT:PID:PL 1/1:0,3:3:9:1|1:13813_T_G:118,9,0 chr1 13838 rs28428499 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.05;QD=31.37;SOR=2.303;VQSLOD=1.99;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:13813_T_G:90,6,0 chr1 14397 rs756427959 CTGT C 37.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.231e+00;ClippingRankSum=0.358;DB;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.49;MQRankSum=1.23;QD=7.55;ReadPosRankSum=-3.580e-01;SOR=0.368;VQSLOD=3.24;culprit=FS GT:AD:DP:GQ:PL 0/1:3,2:5:75:75,0,152 chr1 14522 . G A 49.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=2.38;ClippingRankSum=-3.650e-01;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.34;MQRankSum=-1.447e+00;QD=4.98;ReadPosRankSum=0.00;SOR=1.329;VQSLOD=-7.834e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:6,4:10:78:78,0,118 chr1 14542 rs1045833 A G 79.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.361;ClippingRankSum=1.16;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.49;MQRankSum=-2.219e+00;QD=8.86;ReadPosRankSum=-7.290e-01;SOR=0.892;VQSLOD=-1.607e-01;culprit=MQ GT:AD:DP:GQ:PL 0/1:4,5:9:90:108,0,90 chr1 14574 rs28503599 A G 78.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.307e+00;ClippingRankSum=-8.760e-01;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.49;MQRankSum=-2.219e+00;QD=8.75;ReadPosRankSum=0.361;SOR=0.892;VQSLOD=0.265;culprit=MQ GT:AD:DP:GQ:PL 0/1:4,5:9:89:107,0,89 chr1 14590 . G A 169.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.22;ClippingRankSum=-8.760e-01;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.49;MQRankSum=-2.219e+00;QD=18.86;ReadPosRankSum=0.876;SOR=0.892;VQSLOD=-3.661e-01;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:4,5:9:99:0|1:14590_G_A:198,0,153 chr1 14599 rs531646671 T A 169.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-1.652e+00;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.49;MQRankSum=-2.219e+00;POSITIVE_TRAIN_SITE;QD=18.86;ReadPosRankSum=0.876;SOR=0.892;VQSLOD=1.12;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:4,5:9:99:0|1:14590_G_A:198,0,153 chr1 14604 rs541940975 A G 194.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.361;ClippingRankSum=0.876;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.49;MQRankSum=-2.219e+00;POSITIVE_TRAIN_SITE;QD=21.64;ReadPosRankSum=0.876;SOR=0.892;VQSLOD=0.878;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:4,5:9:99:0|1:14590_G_A:223,0,150 chr1 14610 . T C 197.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=1.20;ClippingRankSum=-1.203e+00;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.26;MQRankSum=-2.054e+00;QD=21.97;ReadPosRankSum=-2.480e-01;SOR=1.402;VQSLOD=-1.758e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:3,6:9:99:0|1:14590_G_A:226,0,108 chr1 14653 rs62635297 C T 135.53 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.747;ClippingRankSum=0.747;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.20;MQRankSum=-7.470e-01;QD=16.94;ReadPosRankSum=0.747;SOR=0.330;VQSLOD=-3.498e-01;culprit=MQ GT:AD:DP:GQ:PL 0/1:1,7:8:3:162,0,3 chr1 14907 rs6682375 A G 153.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-9.290e-01;ClippingRankSum=2.18;DB;DP=12;ExcessHet=3.0103;FS=6.818;MLEAC=1;MLEAF=0.500;MQ=24.36;MQRankSum=2.64;QD=12.81;ReadPosRankSum=-8.250e-01;SOR=0.039;VQSLOD=-3.362e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:4,8:12:75:182,0,75 chr1 14930 rs6682385 A G 142.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.386e+00;ClippingRankSum=0.296;DB;DP=10;ExcessHet=3.0103;FS=3.233;MLEAC=1;MLEAF=0.500;MQ=24.23;MQRankSum=2.17;POSITIVE_TRAIN_SITE;QD=14.28;ReadPosRankSum=-2.960e-01;SOR=0.093;VQSLOD=-1.801e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:3,7:10:99:171,0,105 chr1 14932 . G T 76.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.546;ClippingRankSum=0.296;DP=10;ExcessHet=3.0103;FS=3.233;MLEAC=1;MLEAF=0.500;MQ=24.23;MQRankSum=-2.166e+00;QD=7.68;ReadPosRankSum=0.296;SOR=2.419;VQSLOD=-3.187e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:7,3:10:99:0|1:14932_G_T:105,0,285 chr1 14937 rs11807796 T C 76.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.166e+00;ClippingRankSum=0.296;DB;DP=10;ExcessHet=3.0103;FS=3.233;MLEAC=1;MLEAF=0.500;MQ=24.23;MQRankSum=-2.166e+00;QD=7.68;ReadPosRankSum=0.296;SOR=2.419;VQSLOD=-3.187e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:7,3:10:99:0|1:14932_G_T:105,0,285 chr1 15118 rs11580262 A G 91.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=22.76;SOR=3.258;VQSLOD=0.163;culprit=QD GT:AD:DP:GQ:PL 1/1:0,4:4:12:119,12,0 chr1 16125 rs201026389 T G 103.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.054e+00;ClippingRankSum=-1.001e+00;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.56;MQRankSum=-5.730e-01;QD=11.53;ReadPosRankSum=-5.730e-01;SOR=1.402;VQSLOD=-6.343e-01;culprit=MQ GT:AD:DP:GQ:PL 0/1:3,6:9:61:132,0,61 chr1 16257 rs11489794 G C 40.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.511;ClippingRankSum=-9.420e-01;DB;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.87;MQRankSum=-9.420e-01;QD=1.41;ReadPosRankSum=1.53;SOR=0.641;VQSLOD=-5.292e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:23,6:29:69:69,0,517 chr1 16288 rs113141985 C G 66.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=1.99;ClippingRankSum=-3.900e-02;DB;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.83;MQRankSum=-3.500e-01;QD=3.18;ReadPosRankSum=0.272;SOR=0.394;VQSLOD=-7.579e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:15,6:21:95:95,0,302 chr1 16298 rs62636498 C T 533.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=21.72;QD=31.40;SOR=1.371;VQSLOD=2.25;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,17:17:51:562,51,0 chr1 16378 rs148220436 T C 156.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.933e+00;ClippingRankSum=-4.000e-01;DB;DP=14;ExcessHet=3.0103;FS=2.363;MLEAC=1;MLEAF=0.500;MQ=24.98;MQRankSum=-1.200e+00;QD=11.20;ReadPosRankSum=-8.000e-01;SOR=1.288;VQSLOD=-2.859e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:5,9:14:99:185,0,104 chr1 16495 rs141130360 G C 466.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.196;ClippingRankSum=0.868;DB;DP=28;ExcessHet=3.0103;FS=4.295;MLEAC=1;MLEAF=0.500;MQ=25.08;MQRankSum=0.868;QD=16.67;ReadPosRankSum=1.32;SOR=0.842;VQSLOD=-2.916e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:6,22:28:77:495,0,77 chr1 16949 rs199745162 A C 171.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.385e+00;ClippingRankSum=0.277;DB;DP=23;ExcessHet=3.0103;FS=1.674;MLEAC=1;MLEAF=0.500;MQ=22.08;MQRankSum=-2.923e+00;POSITIVE_TRAIN_SITE;QD=7.47;ReadPosRankSum=1.32;SOR=1.270;VQSLOD=-1.747e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:12,11:23:99:200,0,284 chr1 17020 rs199740902 G A 104.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.585;ClippingRankSum=-1.043e+00;DB;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.72;MQRankSum=-4.830e-01;QD=3.74;ReadPosRankSum=-1.704e+00;SOR=0.551;VQSLOD=-1.160e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:20,8:28:99:133,0,523 chr1 17385 rs201535981 G A 81.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.169;ClippingRankSum=1.18;DB;DP=32;ExcessHet=3.0103;FS=16.414;MLEAC=1;MLEAF=0.500;MQ=40.05;MQRankSum=-4.100e-01;NEGATIVE_TRAIN_SITE;QD=2.56;ReadPosRankSum=-6.040e-01;SOR=1.039;VQSLOD=-3.316e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:26,6:32:99:110,0,729 chr1 17407 rs372841554 G A 99.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.60;ClippingRankSum=-8.660e-01;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.17;MQRankSum=-3.770e-01;NEGATIVE_TRAIN_SITE;QD=2.63;ReadPosRankSum=0.791;SOR=0.693;VQSLOD=-4.813e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:31,7:38:99:128,0,783 chr1 17614 rs201057270 G A 78.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.28;ClippingRankSum=-2.380e-01;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=39.87;MQRankSum=-6.450e-01;QD=3.15;ReadPosRankSum=0.306;SOR=0.307;VQSLOD=1.07;culprit=QD GT:AD:DP:GQ:PL 0/1:20,5:25:99:107,0,572 chr1 17626 . G A 41.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.50;ClippingRankSum=0.203;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=39.59;MQRankSum=-7.710e-01;NEGATIVE_TRAIN_SITE;QD=1.82;ReadPosRankSum=-4.100e-02;SOR=0.061;VQSLOD=0.429;culprit=QD GT:AD:DP:GQ:PL 0/1:19,4:23:70:70,0,539 chr1 20158 . A C 34.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-6.700e-02;ClippingRankSum=-7.620e-01;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.28;MQRankSum=-1.666e+00;QD=3.86;ReadPosRankSum=-1.666e+00;SOR=0.132;VQSLOD=-3.282e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:7,2:9:63:0|1:20158_A_C:63,0,288 chr1 20166 . A G 34.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.666e+00;ClippingRankSum=-6.700e-02;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.28;MQRankSum=-1.179e+00;QD=3.86;ReadPosRankSum=-1.666e+00;SOR=0.132;VQSLOD=-3.048e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:7,2:9:63:0|1:20158_A_C:63,0,288 chr1 20191 rs369546232 T G 70.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.06;ClippingRankSum=-1.061e+00;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.19;MQRankSum=-2.239e+00;QD=6.43;ReadPosRankSum=-1.180e-01;SOR=0.086;VQSLOD=-1.408e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:9,2:11:99:0|1:20158_A_C:99,0,369 chr1 20207 . G A 67.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.45;ClippingRankSum=-2.540e-01;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.81;MQRankSum=-1.775e+00;QD=5.21;ReadPosRankSum=0.085;SOR=0.124;VQSLOD=0.378;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:10,3:13:96:0|1:20158_A_C:96,0,416 chr1 20212 . A G 64.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.437e+00;ClippingRankSum=-8.500e-02;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.81;MQRankSum=-1.944e+00;QD=4.98;ReadPosRankSum=0.592;SOR=0.124;VQSLOD=0.336;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:10,3:13:93:0|1:20158_A_C:93,0,458 chr1 20227 . T A 67.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.44;ClippingRankSum=-2.540e-01;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.81;MQRankSum=-1.606e+00;QD=5.21;ReadPosRankSum=1.27;SOR=0.495;VQSLOD=0.752;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:10,3:13:96:0|1:20158_A_C:96,0,416 chr1 20250 rs373030326 T C 183.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.034e+00;ClippingRankSum=-6.780e-01;DB;DP=11;ExcessHet=3.0103;FS=4.393;MLEAC=1;MLEAF=0.500;MQ=30.52;MQRankSum=-2.520e+00;QD=16.71;ReadPosRankSum=-8.960e-01;SOR=2.833;VQSLOD=-3.094e+00;culprit=SOR GT:AD:DP:GQ:PL 0/1:4,7:11:99:212,0,126 chr1 20316 . GA G 102.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;ClippingRankSum=0.322;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.79;MQRankSum=-1.920e+00;QD=12.84;ReadPosRankSum=0.322;SOR=0.799;VQSLOD=3.22;culprit=FS GT:AD:DP:GQ:PL 0/1:3,5:8:47:140,0,47 chr1 20620 rs746313125 C T 30.74 VQSRTrancheSNP99.95to100.00 AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=24.00;QD=15.37;SOR=2.303;VQSLOD=-3.789e+00;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:58,6,0 chr1 28494 rs768288163 T C 46.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.580e-01;ClippingRankSum=1.23;DB;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.74;MQRankSum=-3.580e-01;QD=9.35;ReadPosRankSum=0.358;SOR=1.609;VQSLOD=-1.634e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:3,2:5:75:0|1:28494_T_C:75,0,120 chr1 28511 rs773821537 G A 68.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-9.880e-01;ClippingRankSum=-4.060e-01;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.46;MQRankSum=-4.060e-01;QD=11.46;ReadPosRankSum=0.406;SOR=0.693;VQSLOD=0.083;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:3,3:6:97:0|1:28494_T_C:97,0,117 chr1 28558 rs371996741 C T 46.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.421;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.48;MQRankSum=-9.220e-01;QD=5.85;ReadPosRankSum=0.922;SOR=0.693;VQSLOD=0.242;culprit=QD GT:AD:DP:GQ:PL 0/1:4,4:8:75:75,0,99 chr1 28563 rs4099234 A G 187.10 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.07;ClippingRankSum=0.572;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.48;MQRankSum=-1.067e+00;QD=23.39;ReadPosRankSum=1.59;SOR=0.693;VQSLOD=-4.658e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:2,6:8:11:215,0,11 chr1 30548 rs62028215 T G 30.74 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.12;NEGATIVE_TRAIN_SITE;QD=15.37;SOR=2.303;VQSLOD=-2.565e+00;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:58,6,0 chr1 39230 rs62637791 G A 473.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.843e+00;ClippingRankSum=2.28;DB;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.23;MQRankSum=1.90;QD=10.77;ReadPosRankSum=-3.760e-01;SOR=0.672;VQSLOD=-3.809e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:21,23:44:99:502,0,519 chr1 39255 rs62637793 A C 393.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.05;ClippingRankSum=-6.800e-02;DB;DP=40;ExcessHet=3.0103;FS=4.677;MLEAC=1;MLEAF=0.500;MQ=27.40;MQRankSum=0.884;QD=9.84;ReadPosRankSum=-1.672e+00;SOR=1.015;VQSLOD=-3.561e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:22,18:40:99:422,0,699 chr1 39261 rs200677948 T C 1142.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.600e-01;ClippingRankSum=0.340;DB;DP=38;ExcessHet=3.0103;FS=1.785;MLEAC=1;MLEAF=0.500;MQ=27.47;MQRankSum=0.100;QD=30.07;ReadPosRankSum=-1.061e+00;SOR=0.307;VQSLOD=-3.538e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:6,32:38:64:1171,0,64 chr1 47960 rs796517829 T A 32.74 VQSRTrancheSNP99.95to100.00 AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=16.37;SOR=2.303;VQSLOD=-3.450e+00;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:60,6,0 chr1 51668 . C A 62.74 PASS AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.35;QD=31.37;SOR=2.303;VQSLOD=2.30;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:51668_C_A:90,6,0 chr1 51673 . T C 62.74 PASS AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.35;QD=31.37;SOR=2.303;VQSLOD=2.66;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:51668_C_A:90,6,0 chr1 52058 rs62637813 G C 124.84 PASS AC=2;AF=1.00;AN=2;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.51;NEGATIVE_TRAIN_SITE;QD=20.81;SOR=2.303;VQSLOD=0.384;culprit=QD GT:AD:DP:GQ:PL 1/1:0,6:6:18:153,18,0 chr1 52238 rs2691277 T G 143.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.35;POSITIVE_TRAIN_SITE;QD=20.54;SOR=0.941;VQSLOD=2.94;culprit=QD GT:AD:DP:GQ:PL 1/1:0,7:7:21:172,21,0 chr1 55164 rs3091274 C A 93.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.35;POSITIVE_TRAIN_SITE;QD=23.26;SOR=0.693;VQSLOD=2.69;culprit=QD GT:AD:DP:GQ:PL 1/1:0,4:4:12:121,12,0 chr1 55299 rs10399749 C T 177.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=46.97;QD=25.40;SOR=1.609;VQSLOD=3.34;culprit=QD GT:AD:DP:GQ:PL 1/1:0,7:7:21:206,21,0 chr1 55326 rs3107975 T C 209.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.18;POSITIVE_TRAIN_SITE;QD=26.22;SOR=1.863;VQSLOD=4.15;culprit=QD GT:AD:DP:GQ:PL 1/1:0,8:8:24:238,24,0 chr1 55545 rs28396308 C T 210.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=38.68;POSITIVE_TRAIN_SITE;QD=30.11;SOR=1.609;VQSLOD=4.48;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,7:7:21:239,21,0 chr1 55926 rs13343114 T C 242.78 PASS AC=2;AF=1.00;AN=2;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.68;QD=26.98;SOR=1.402;VQSLOD=3.26;culprit=QD GT:AD:DP:GQ:PL 1/1:0,9:9:27:271,27,0 chr1 56987 . C CA 59.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.13;ClippingRankSum=-6.800e-01;DP=16;ExcessHet=3.0103;FS=2.663;MLEAC=1;MLEAF=0.500;MQ=52.05;MQRankSum=-3.172e+00;NEGATIVE_TRAIN_SITE;QD=3.73;ReadPosRankSum=0.453;SOR=1.445;VQSLOD=-1.063e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:11,5:16:97:97,0,282 chr1 57158 rs6658003 G C 298.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.90;ClippingRankSum=-8.030e-01;DB;DP=19;ExcessHet=3.0103;FS=9.745;MLEAC=1;MLEAF=0.500;MQ=41.32;MQRankSum=2.32;NEGATIVE_TRAIN_SITE;QD=15.72;ReadPosRankSum=-3.800e-01;SOR=0.027;VQSLOD=-1.433e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:7,12:19:99:327,0,136 chr1 57292 rs201418760 C T 301.77 PASS AC=2;AF=1.00;AN=2;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.40;POSITIVE_TRAIN_SITE;QD=30.18;SOR=1.085;VQSLOD=5.32;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,10:10:30:330,30,0 chr1 57856 rs199609147 T A 43.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.550;ClippingRankSum=-5.500e-01;DB;DP=7;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=38.46;MQRankSum=0.00;NEGATIVE_TRAIN_SITE;QD=6.25;ReadPosRankSum=-5.500e-01;SOR=2.833;VQSLOD=-2.017e+00;culprit=SOR GT:AD:DP:GQ:PL 0/1:4,3:7:72:72,0,90 chr1 57952 rs2691334 A C 36.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=27.00;QD=18.37;SOR=0.693;VQSLOD=-1.067e-01;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:64,6,0 chr1 58211 rs2691335 A G 120.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=24.18;SOR=3.611;VQSLOD=0.896;culprit=QD GT:AD:DP:GQ:PL 1/1:0,5:5:15:149,15,0 chr1 58771 rs75024357 T C 147.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.135;ClippingRankSum=-2.440e-01;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.74;MQRankSum=-5.290e-01;QD=12.31;ReadPosRankSum=-2.440e-01;SOR=1.085;VQSLOD=1.15;culprit=MQ GT:AD:DP:GQ:PL 0/1:5,7:12:99:176,0,109 chr1 61442 rs2531261 A G 281.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=35.84;QD=25.62;SOR=1.802;VQSLOD=2.27;culprit=QD GT:AD:DP:GQ:PL 1/1:0,11:11:33:310,33,0 chr1 61987 rs76735897 A G 250.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.290e-01;ClippingRankSum=0.380;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.54;MQRankSum=-1.000e+00;QD=20.90;ReadPosRankSum=0.831;SOR=0.754;VQSLOD=1.98;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:5,7:12:99:0|1:61987_A_G:279,0,301 chr1 61989 rs77573425 G C 250.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.977e+00;ClippingRankSum=-8.310e-01;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.54;MQRankSum=-5.290e-01;QD=20.90;ReadPosRankSum=1.31;SOR=0.754;VQSLOD=1.90;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:5,7:12:99:0|1:61987_A_G:279,0,301 chr1 62777 rs3844233 A T 89.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.680;ClippingRankSum=-3.400e-01;DB;DP=16;ExcessHet=3.0103;FS=5.237;MLEAC=1;MLEAF=0.500;MQ=36.64;MQRankSum=1.02;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=5.61;ReadPosRankSum=0.113;SOR=0.681;VQSLOD=-4.953e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:11,5:16:99:118,0,303 chr1 63516 rs62639101 A G 66.90 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-7.360e-01;ClippingRankSum=0.736;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.00;MQRankSum=-7.360e-01;QD=11.15;ReadPosRankSum=-7.360e-01;SOR=0.368;VQSLOD=-2.648e-01;culprit=MQ GT:AD:DP:GQ:PL 0/1:1,5:6:15:95,0,15 chr1 63527 rs62639102 T C 133.84 PASS AC=2;AF=1.00;AN=2;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=27.00;QD=22.31;SOR=1.329;VQSLOD=0.356;culprit=QD GT:AD:DP:GQ:PL 1/1:0,6:6:18:162,18,0 chr1 63697 rs111440589 T C 32.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;ClippingRankSum=1.00;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.66;MQRankSum=0.248;QD=3.64;ReadPosRankSum=0.248;SOR=0.593;VQSLOD=0.878;culprit=QD GT:AD:DP:GQ:PL 0/1:6,3:9:61:61,0,135 chr1 64512 rs574185548 TG T 114.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.421;ClippingRankSum=0.00;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=38.62;MQRankSum=0.922;POSITIVE_TRAIN_SITE;QD=14.34;ReadPosRankSum=1.75;SOR=0.693;VQSLOD=4.77;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 0/1:4,4:8:99:0|1:64512_TG_T:152,0,156 chr1 64518 rs567315672 G T 123.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.017e+00;ClippingRankSum=-1.638e+00;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=38.62;MQRankSum=0.421;POSITIVE_TRAIN_SITE;QD=15.47;ReadPosRankSum=1.64;SOR=0.693;VQSLOD=2.73;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:4,4:8:99:0|1:64512_TG_T:152,0,156 chr1 64548 rs771510052 A C 205.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.590e-01;ClippingRankSum=-2.590e-01;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=44.87;MQRankSum=-4.670e-01;NEGATIVE_TRAIN_SITE;QD=17.15;ReadPosRankSum=0.259;SOR=1.863;VQSLOD=-8.758e-01;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:6,6:12:99:0|1:64548_A_C:234,0,234 chr1 64552 rs749441654 G A 202.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.010e-01;ClippingRankSum=1.20;DB;DP=13;ExcessHet=3.0103;FS=3.358;MLEAC=1;MLEAF=0.500;MQ=44.73;MQRankSum=-9.350e-01;NEGATIVE_TRAIN_SITE;QD=15.60;ReadPosRankSum=1.20;SOR=2.584;VQSLOD=-1.656e+00;culprit=SOR GT:AD:DP:GQ:PGT:PID:PL 0/1:7,6:13:99:0|1:64548_A_C:231,0,254 chr1 70728 . C T 45.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-1.380e+00;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.04;MQRankSum=-1.380e+00;QD=7.63;ReadPosRankSum=1.38;SOR=1.609;VQSLOD=-1.606e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:2,4:6:32:74,0,32 chr1 70761 . T C 63.85 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-7.310e-01;ClippingRankSum=-7.310e-01;DP=5;ExcessHet=3.0103;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=24.63;MQRankSum=-7.310e-01;QD=12.77;ReadPosRankSum=-7.310e-01;SOR=1.447;VQSLOD=-3.148e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:1,4:5:17:92,0,17 chr1 71875 rs12402780 G A 32.74 VQSRTrancheSNP99.95to100.00 AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=16.37;SOR=2.303;VQSLOD=-3.135e+00;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:60,6,0 chr1 72862 . G A 115.90 PASS AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=24.00;QD=23.18;SOR=3.611;VQSLOD=-3.843e-01;culprit=QD GT:AD:DP:GQ:PL 1/1:0,5:5:15:144,15,0 chr1 74681 rs13328683 G T 34.74 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=32.63;NEGATIVE_TRAIN_SITE;QD=17.37;SOR=2.303;VQSLOD=-2.113e+00;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:62,6,0 chr1 76610 . C A 56.28 VQSRTrancheSNP99.80to99.90 AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.40;QD=18.76;SOR=1.179;VQSLOD=-1.200e+00;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,3:3:9:84,9,0 chr1 84133 rs201488854 A T 136.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.135;ClippingRankSum=-2.440e-01;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.94;MQRankSum=0.135;QD=11.40;ReadPosRankSum=0.689;SOR=0.631;VQSLOD=1.98;culprit=MQ GT:AD:DP:GQ:PL 0/1:5,7:12:99:165,0,99 chr1 84214 . AT A 85.25 PASS AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.37;QD=28.42;SOR=2.833;VQSLOD=2.66;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 1/1:0,3:3:9:1|1:84214_AT_A:122,9,0 chr1 84230 . T C 94.28 PASS AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.67;QD=34.24;SOR=2.303;VQSLOD=2.28;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:9:1|1:84214_AT_A:122,9,0 chr1 94271 rs200715572 C G 170.78 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.54;QD=21.35;SOR=4.407;VQSLOD=-2.778e+00;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,8:8:24:199,24,0 chr1 94570 rs200113991 T G 46.94 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-7.270e-01;ClippingRankSum=0.727;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.72;MQRankSum=0.727;QD=11.73;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=-3.782e-01;culprit=MQ GT:AD:DP:GQ:PL 0/1:1,3:4:14:75,0,14 chr1 97953 rs201609557 A G 57.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.055e+00;ClippingRankSum=0.158;DB;DP=17;ExcessHet=3.0103;FS=12.797;MLEAC=1;MLEAF=0.500;MQ=23.45;MQRankSum=-4.740e-01;QD=3.40;ReadPosRankSum=-1.580e-01;SOR=0.591;VQSLOD=-4.415e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:12,5:17:86:86,0,288 chr1 98311 . C T 46.28 VQSRTrancheSNP99.95to100.00 AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.00;QD=15.43;SOR=2.833;VQSLOD=-4.752e+00;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,3:3:9:74,9,0 chr1 98683 rs796405068 G A 57.94 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=-7.270e-01;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.57;MQRankSum=0.727;NEGATIVE_TRAIN_SITE;QD=14.48;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=-7.910e-01;culprit=DP GT:AD:DP:GQ:PL 0/1:1,3:4:14:86,0,14 chr1 98999 rs376621245 T TTTTA 187.87 PASS AC=2;AF=1.00;AN=2;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.64;QD=30.63;SOR=1.981;VQSLOD=4.20;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:225,15,0 chr1 99166 rs78627600 C T 58.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.75;ClippingRankSum=-4.040e-01;DB;DP=16;ExcessHet=3.0103;FS=2.769;MLEAC=1;MLEAF=0.500;MQ=38.58;MQRankSum=0.135;NEGATIVE_TRAIN_SITE;QD=3.67;ReadPosRankSum=0.135;SOR=1.609;VQSLOD=-1.674e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:13,3:16:87:0|1:99166_C_T:87,0,675 chr1 99180 rs201323924 T C 61.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.361;ClippingRankSum=0.072;DB;DP=15;ExcessHet=3.0103;FS=2.869;MLEAC=1;MLEAF=0.500;MQ=38.75;MQRankSum=0.650;NEGATIVE_TRAIN_SITE;QD=4.12;ReadPosRankSum=0.938;SOR=1.781;VQSLOD=-1.766e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:12,3:15:90:0|1:99166_C_T:90,0,651 chr1 99665 rs368526587 C T 55.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.06;POSITIVE_TRAIN_SITE;QD=18.43;SOR=2.833;VQSLOD=-6.598e-01;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,3:3:9:83,9,0 chr1 99874 rs62642104 C T 84.03 VQSRTrancheSNP99.80to99.90 AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.30;QD=21.01;SOR=3.258;VQSLOD=-1.686e+00;culprit=QD GT:AD:DP:GQ:PL 1/1:0,4:4:12:112,12,0 chr1 99887 rs62642105 C G 84.03 VQSRTrancheSNP99.80to99.90 AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.30;QD=21.01;SOR=3.258;VQSLOD=-1.108e+00;culprit=QD GT:AD:DP:GQ:PL 1/1:0,4:4:12:112,12,0 chr1 101268 rs375749629 G A 144.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;ClippingRankSum=0.573;DB;DP=9;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=34.57;MQRankSum=0.573;NEGATIVE_TRAIN_SITE;QD=16.09;ReadPosRankSum=0.248;SOR=3.126;VQSLOD=-2.961e+00;culprit=SOR GT:AD:DP:GQ:PL 0/1:3,6:9:63:173,0,63 chr1 101393 . T C 141.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.342;ClippingRankSum=0.830;DP=17;ExcessHet=3.0103;FS=9.971;MLEAC=1;MLEAF=0.500;MQ=34.86;MQRankSum=-1.025e+00;NEGATIVE_TRAIN_SITE;QD=8.34;ReadPosRankSum=-1.025e+00;SOR=0.472;VQSLOD=-2.233e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:10,7:17:99:170,0,258 chr1 102138 rs374391784 C T 46.28 VQSRTrancheSNP99.95to100.00 AC=2;AF=1.00;AN=2;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.00;QD=15.43;SOR=2.833;VQSLOD=-4.468e+00;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,3:3:9:74,9,0 chr1 102951 rs200298631 C T 141.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-9.370e-01;ClippingRankSum=0.117;DB;DP=34;ExcessHet=3.0103;FS=1.739;MLEAC=1;MLEAF=0.500;MQ=41.58;MQRankSum=1.09;NEGATIVE_TRAIN_SITE;QD=4.17;ReadPosRankSum=0.039;SOR=0.319;VQSLOD=-2.185e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:25,9:34:99:170,0,675 chr1 103207 rs373871696 A G 41.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-7.850e-01;ClippingRankSum=0.488;DB;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.38;MQRankSum=-2.760e-01;QD=1.16;ReadPosRankSum=1.21;SOR=0.269;VQSLOD=-1.576e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:30,6:36:70:70,0,774 chr1 103241 rs62642109 C T 681.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=3.57;ClippingRankSum=0.415;DB;DP=27;ExcessHet=3.0103;FS=5.863;MLEAC=1;MLEAF=0.500;MQ=29.60;MQRankSum=-5.260e-01;QD=25.25;ReadPosRankSum=0.581;SOR=3.611;VQSLOD=-4.683e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:7,20:27:99:710,0,120 chr1 103250 rs796779951 G A 277.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.245;ClippingRankSum=0.517;DB;DP=25;ExcessHet=3.0103;FS=3.188;MLEAC=1;MLEAF=0.500;MQ=29.97;MQRankSum=0.462;QD=11.11;ReadPosRankSum=1.17;SOR=1.863;VQSLOD=-2.629e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:12,13:25:99:306,0,441 chr1 103905 rs62642112 A G 33.74 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=35.78;NEGATIVE_TRAIN_SITE;QD=16.87;SOR=2.303;VQSLOD=-2.163e+00;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 chr1 104033 rs4287120 T C 279.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.396;ClippingRankSum=-1.700e-01;DB;DP=17;ExcessHet=3.0103;FS=2.197;MLEAC=1;MLEAF=0.500;MQ=33.08;MQRankSum=-2.830e-01;NEGATIVE_TRAIN_SITE;QD=16.46;ReadPosRankSum=1.76;SOR=0.283;VQSLOD=-1.954e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:4,13:17:73:308,0,73 chr1 104072 . C T 31.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.56;ClippingRankSum=0.00;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.06;MQRankSum=0.623;NEGATIVE_TRAIN_SITE;QD=2.27;ReadPosRankSum=1.40;SOR=1.093;VQSLOD=0.148;culprit=QD GT:AD:DP:GQ:PL 0/1:11,3:14:60:60,0,228 chr1 105445 . G A 30.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.060e-01;ClippingRankSum=0.406;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.00;MQRankSum=0.406;QD=5.13;ReadPosRankSum=-9.880e-01;SOR=0.132;VQSLOD=-1.386e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:3,3:6:59:59,0,65 chr1 105700 . T G 51.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.775e+00;ClippingRankSum=0.592;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.92;MQRankSum=0.423;QD=3.98;ReadPosRankSum=0.930;SOR=0.223;VQSLOD=-4.361e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:10,3:13:80:0|1:105700_T_G:80,0,390 chr1 105702 . A G 51.77 VQSRTrancheSNP99.50to99.60 AC=1;AF=0.500;AN=2;BaseQRankSum=0.423;ClippingRankSum=-7.610e-01;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.92;MQRankSum=1.44;QD=3.98;ReadPosRankSum=0.930;SOR=0.223;VQSLOD=-6.941e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:10,3:13:80:0|1:105700_T_G:80,0,390 chr1 105890 rs200280933 G A 110.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.572;ClippingRankSum=-1.589e+00;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.51;MQRankSum=-5.720e-01;QD=13.85;ReadPosRankSum=-5.720e-01;SOR=1.863;VQSLOD=-3.109e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:2,6:8:30:139,0,30 chr1 108297 rs201078696 A C 91.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=1.23;ClippingRankSum=-1.231e+00;DB;DP=5;ExcessHet=3.0103;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=26.78;MQRankSum=0.358;QD=18.35;ReadPosRankSum=1.23;SOR=0.859;VQSLOD=-2.984e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:2,3:5:39:0|1:108297_A_C:120,0,39 chr1 108310 rs74747225 T C 91.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=-3.580e-01;DB;DP=5;ExcessHet=3.0103;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=26.78;MQRankSum=0.358;QD=18.35;ReadPosRankSum=1.23;SOR=0.859;VQSLOD=-2.984e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:2,3:5:39:0|1:108297_A_C:120,0,39 chr1 108365 rs79073610 A G 90.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.219e+00;ClippingRankSum=-8.760e-01;DB;DP=9;ExcessHet=3.0103;FS=13.222;MLEAC=1;MLEAF=0.500;MQ=32.16;MQRankSum=2.22;NEGATIVE_TRAIN_SITE;QD=10.09;ReadPosRankSum=-3.610e-01;SOR=3.590;VQSLOD=-3.000e+00;culprit=SOR GT:AD:DP:GQ:PL 0/1:4,5:9:89:119,0,89 chr1 108413 rs200678306 T G 67.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.400e-01;ClippingRankSum=0.340;DB;DP=16;ExcessHet=3.0103;FS=11.994;MLEAC=1;MLEAF=0.500;MQ=32.02;MQRankSum=-2.945e+00;NEGATIVE_TRAIN_SITE;QD=4.24;ReadPosRankSum=-1.020e+00;SOR=0.594;VQSLOD=-3.137e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:11,5:16:96:96,0,327 chr1 110703 . C T 347.85 VQSRTrancheSNP99.95to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=-3.470e-01;ClippingRankSum=1.50;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.04;MQRankSum=0.810;QD=23.19;ReadPosRankSum=-3.470e-01;SOR=4.047;VQSLOD=-6.484e+00;culprit=QD GT:AD:DP:GQ:PL 1/1:1,14:15:17:376,17,0 chr1 110752 . C A 60.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.98;ClippingRankSum=-3.700e-02;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.50;MQRankSum=1.45;QD=2.64;ReadPosRankSum=-8.570e-01;SOR=1.179;VQSLOD=-1.354e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:18,5:23:89:89,0,392 chr1 111371 rs796221635 A G 119.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=23.98;SOR=3.611;VQSLOD=0.203;culprit=QD GT:AD:DP:GQ:PL 1/1:0,5:5:15:148,15,0 chr1 113682 rs368487483 A G 257.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.06;QD=23.43;SOR=0.859;VQSLOD=-1.672e-01;culprit=QD GT:AD:DP:GQ:PL 1/1:0,11:11:33:286,33,0 chr1 113969 . C T 231.77 VQSRTrancheSNP99.80to99.90 AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.67;QD=23.18;SOR=3.258;VQSLOD=-1.257e+00;culprit=QD GT:AD:DP:GQ:PL 1/1:0,10:10:30:260,30,0 chr1 115779 . T C 109.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.867;ClippingRankSum=-1.387e+00;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.39;MQRankSum=1.39;QD=4.22;ReadPosRankSum=0.347;SOR=0.631;VQSLOD=0.903;culprit=QD GT:AD:DP:GQ:PL 0/1:19,7:26:99:138,0,481 chr1 118617 rs372912307 T C 395.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.14;QD=24.74;SOR=0.941;VQSLOD=1.51;culprit=QD GT:AD:DP:GQ:PL 1/1:0,16:16:48:424,48,0 chr1 120983 rs182468771 C T 74.79 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=-7.270e-01;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=44.45;MQRankSum=0.727;QD=18.70;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=1.48;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 0/1:1,3:4:23:0|1:120983_C_T:103,0,23 chr1 121009 rs1851943 C T 89.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.28;QD=29.76;SOR=1.179;VQSLOD=3.58;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,3:3:9:1|1:120983_C_T:117,9,0 chr1 123511 rs377389630 G A 140.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=1.24;ClippingRankSum=-6.000e-01;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.63;MQRankSum=1.24;QD=11.73;ReadPosRankSum=1.24;SOR=1.445;VQSLOD=-1.729e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:4,8:12:48:169,0,48 chr1 123642 rs370064167 T G 217.90 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.28;ClippingRankSum=1.68;DB;DP=13;ExcessHet=3.0103;FS=3.736;MLEAC=1;MLEAF=0.500;MQ=24.02;MQRankSum=-2.960e-01;QD=16.76;ReadPosRankSum=0.888;SOR=2.494;VQSLOD=-3.653e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:2,11:13:15:246,0,15 chr1 126113 rs79114531 C A 436.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.66;QD=29.12;SOR=2.448;VQSLOD=2.82;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,15:15:45:465,45,0 chr1 127491 rs368732900 T G 152.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-6.880e-01;ClippingRankSum=1.43;DB;DP=36;ExcessHet=3.0103;FS=7.399;MLEAC=1;MLEAF=0.500;MQ=23.39;MQRankSum=-1.170e-01;QD=4.24;ReadPosRankSum=0.856;SOR=1.329;VQSLOD=-3.954e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:24,12:36:99:181,0,492 chr1 127573 rs199894737 G A 269.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;ClippingRankSum=-3.330e-01;DB;DP=42;ExcessHet=3.0103;FS=1.286;MLEAC=1;MLEAF=0.500;MQ=25.40;MQRankSum=-1.020e-01;QD=6.42;ReadPosRankSum=0.794;SOR=0.387;VQSLOD=-3.778e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:25,17:42:99:298,0,441 chr1 127909 . G A 43.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=-3.580e-01;DP=6;ExcessHet=3.0103;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=25.36;MQRankSum=1.23;QD=8.75;ReadPosRankSum=-1.231e+00;SOR=0.859;VQSLOD=-3.237e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:2,3:5:34:72,0,34 chr1 128798 rs376726476 C T 199.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.55;QD=28.54;SOR=1.609;VQSLOD=2.75;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,7:7:21:228,21,0 chr1 129010 rs377161483 AATG A 322.75 PASS AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=31.62;POSITIVE_TRAIN_SITE;QD=29.09;SOR=0.693;VQSLOD=5.96;culprit=FS GT:AD:DP:GQ:PL 1/1:0,8:8:24:360,24,0 chr1 129285 rs372768449 G A 483.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.14;QD=24.19;SOR=2.531;VQSLOD=0.398;culprit=QD GT:AD:DP:GQ:PL 1/1:0,20:20:60:512,60,0 chr1 131552 rs371080566 G T 51.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.550;ClippingRankSum=0.550;DB;DP=7;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=20.29;MQRankSum=0.00;QD=7.40;ReadPosRankSum=0.00;SOR=0.061;VQSLOD=-3.852e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:3,4:7:53:80,0,53 chr1 133129 rs367730352 G A 556.77 PASS AC=2;AF=1.00;AN=2;DB;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.63;QD=30.93;SOR=3.500;VQSLOD=1.73;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,18:18:54:585,54,0 chr1 133483 rs369820305 G T 502.84 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.26;ClippingRankSum=-1.037e+00;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.38;MQRankSum=0.382;QD=21.86;ReadPosRankSum=-6.000e-01;SOR=0.638;VQSLOD=0.151;culprit=QD GT:AD:DP:GQ:PL 1/1:2,21:23:18:531,18,0 chr1 134876 rs375850923 C T 66.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.610e-01;ClippingRankSum=0.729;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.46;MQRankSum=0.361;QD=7.42;ReadPosRankSum=0.00;SOR=0.527;VQSLOD=1.05;culprit=MQ GT:AD:DP:GQ:PL 0/1:5,4:9:95:95,0,100 chr1 136048 rs371677125 C T 577.77 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=0.763;ClippingRankSum=-3.470e-01;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.50;MQRankSum=-1.179e+00;QD=23.11;ReadPosRankSum=0.069;SOR=0.818;VQSLOD=-5.380e-01;culprit=QD GT:AD:DP:GQ:PL 1/1:1,24:25:41:606,41,0 chr1 136644 rs370365546 AG A 142 PASS AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.93;SOR=1.609;VQSLOD=3.73;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 1/1:0,4:4:12:1|1:136644_AG_A:179,12,0 chr1 136652 . A G 135.89 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;ClippingRankSum=1.38;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=22.65;ReadPosRankSum=1.38;SOR=0.368;VQSLOD=13.88;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:2,4:6:2:0|1:136644_AG_A:162,0,2 chr1 136817 rs375833141 T C 111.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=-5.370e-01;ClippingRankSum=-9.270e-01;DB;DP=18;ExcessHet=3.0103;FS=2.062;MLEAC=1;MLEAF=0.500;MQ=47.94;MQRankSum=0.927;NEGATIVE_TRAIN_SITE;QD=6.57;ReadPosRankSum=1.12;SOR=0.223;VQSLOD=-1.032e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:7,10:17:99:140,0,111 chr1 136962 rs373582709 C T 108.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.368;ClippingRankSum=0.053;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=38.38;MQRankSum=0.788;QD=6.80;ReadPosRankSum=1.21;SOR=0.293;VQSLOD=1.14;culprit=QD GT:AD:DP:GQ:PL 0/1:8,8:16:99:137,0,127 chr1 137287 rs375144581 G A 76.03 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.00;QD=19.01;SOR=3.258;VQSLOD=-2.663e+00;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,4:4:12:104,12,0 chr1 137622 rs376555721 G A 125.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-6.480e-01;ClippingRankSum=-5.900e-02;DB;DP=15;ExcessHet=3.0103;FS=15.564;MLEAC=1;MLEAF=0.500;MQ=20.58;MQRankSum=1.12;QD=8.38;ReadPosRankSum=1.24;SOR=1.126;VQSLOD=-4.624e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:6,9:15:99:154,0,104 chr1 137825 rs147252685 G A 568.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=-7.450e-01;ClippingRankSum=-1.875e+00;DB;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.91;MQRankSum=-6.800e-02;NEGATIVE_TRAIN_SITE;QD=16.73;ReadPosRankSum=-1.333e+00;SOR=0.836;VQSLOD=-9.551e-01;culprit=MQ GT:AD:DP:GQ:PL 0/1:6,28:34:64:597,0,64 chr1 138156 rs370691115 G T 567.77 PASS AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.35;QD=23.66;SOR=0.859;VQSLOD=-4.853e-01;culprit=QD GT:AD:DP:GQ:PL 1/1:0,24:24:71:596,71,0 chr1 139781 rs371864317 G A 71.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.15;QD=23.76;SOR=2.833;VQSLOD=1.65;culprit=QD GT:AD:DP:GQ:PL 1/1:0,3:3:9:99,9,0 chr1 150462 rs199583388 A C 75.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.68;QD=25.09;SOR=2.833;VQSLOD=2.12;culprit=QD GT:AD:DP:GQ:PL 1/1:0,3:3:9:103,9,0 chr1 159030 . ACC A 37.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.231e+00;ClippingRankSum=0.358;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.73;MQRankSum=1.23;QD=7.55;ReadPosRankSum=0.358;SOR=0.368;VQSLOD=3.23;culprit=FS GT:AD:DP:GQ:PL 0/1:3,2:5:40:75,0,40 chr1 173098 rs370188889 C T 186.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.89;QD=23.35;SOR=2.833;VQSLOD=0.294;culprit=QD GT:AD:DP:GQ:PL 1/1:0,8:8:24:215,24,0 chr1 180958 . CCCCTAA C 40.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.03;ClippingRankSum=-1.026e+00;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=38.57;MQRankSum=0.00;NEGATIVE_TRAIN_SITE;QD=10.18;ReadPosRankSum=1.03;SOR=2.303;VQSLOD=-7.099e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:59:78,0,59 chr1 181022 . C T 64.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=2.18;ClippingRankSum=0.00;DP=19;ExcessHet=3.0103;FS=6.532;MLEAC=1;MLEAF=0.500;MQ=40.43;MQRankSum=0.825;NEGATIVE_TRAIN_SITE;QD=5.40;ReadPosRankSum=-2.890e-01;SOR=1.431;VQSLOD=-1.501e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:8,4:12:93:93,0,147 chr1 181113 . A G 630.77 PASS AC=2;AF=1.00;AN=2;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.48;QD=31.54;SOR=3.056;VQSLOD=1.72;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,20:20:60:659,60,0 chr1 181393 . G C 61.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-6.650e-01;ClippingRankSum=-1.155e+00;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.50;MQRankSum=-1.155e+00;QD=2.69;ReadPosRankSum=0.315;SOR=0.593;VQSLOD=1.97;culprit=QD GT:AD:DP:GQ:PL 0/1:17,6:23:90:90,0,417 chr1 181481 . AG A 110.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.139e+00;ClippingRankSum=0.813;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.46;MQRankSum=-4.880e-01;QD=6.92;ReadPosRankSum=0.380;SOR=0.883;VQSLOD=3.17;culprit=FS GT:AD:DP:GQ:PL 0/1:10,6:16:99:148,0,277 chr1 181910 . T A 321.78 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;ClippingRankSum=-1.182e+00;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.17;MQRankSum=-9.670e-01;NEGATIVE_TRAIN_SITE;QD=26.81;ReadPosRankSum=1.18;SOR=0.693;VQSLOD=0.541;culprit=QD GT:AD:DP:GQ:PL 0/1:2,10:12:27:350,0,27 chr1 182095 . T C 416.77 PASS AC=2;AF=1.00;AN=2;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.19;QD=26.05;SOR=2.584;VQSLOD=1.27;culprit=QD GT:AD:DP:GQ:PL 1/1:0,16:16:48:445,48,0 chr1 182291 . G A 87.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.79;ClippingRankSum=-5.290e-01;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.34;MQRankSum=1.00;QD=7.31;ReadPosRankSum=-5.290e-01;SOR=0.412;VQSLOD=-5.537e-01;culprit=MQ GT:AD:DP:GQ:PL 0/1:7,5:12:99:116,0,144 chr1 182903 . C G 108.90 PASS AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.63;QD=21.78;SOR=1.981;VQSLOD=0.099;culprit=QD GT:AD:DP:GQ:PL 1/1:0,5:5:15:137,15,0 chr1 184413 . C A 1078.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.540e-01;ClippingRankSum=-1.780e+00;DP=70;ExcessHet=3.0103;FS=4.934;MLEAC=1;MLEAF=0.500;MQ=42.66;MQRankSum=0.102;NEGATIVE_TRAIN_SITE;QD=15.41;ReadPosRankSum=1.37;SOR=1.351;VQSLOD=-5.146e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:28,42:70:99:1107,0,710 chr1 185194 . G C 545.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.960e-01;ClippingRankSum=-1.912e+00;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.68;MQRankSum=3.04;QD=18.19;ReadPosRankSum=-3.430e-01;SOR=1.121;VQSLOD=-2.234e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:7,23:30:99:574,0,111 chr1 185336 . C T 80.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.591;ClippingRankSum=-1.063e+00;DP=31;ExcessHet=3.0103;FS=11.800;MLEAC=1;MLEAF=0.500;MQ=24.62;MQRankSum=-1.724e+00;QD=2.61;ReadPosRankSum=3.10;SOR=3.567;VQSLOD=-4.438e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:24,7:31:99:109,0,562 chr1 185428 . A G 626.79 VQSRTrancheSNP99.95to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=0.241;ClippingRankSum=-5.290e-01;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=24.78;MQRankSum=2.07;QD=24.11;ReadPosRankSum=-4.800e-02;SOR=2.833;VQSLOD=-5.186e+00;culprit=QD GT:AD:DP:GQ:PL 1/1:2,24:26:22:655,22,0 chr1 185451 . A G 619.77 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.01;QD=28.17;SOR=4.804;VQSLOD=-2.596e+00;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,22:22:66:648,66,0 chr1 185761 . G GGGGCCA 31.73 VQSRTrancheINDEL95.00to96.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.198;ClippingRankSum=-9.220e-01;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.46;MQRankSum=-9.220e-01;QD=4.53;ReadPosRankSum=-1.980e-01;SOR=1.802;VQSLOD=0.961;culprit=FS GT:AD:DP:GQ:PL 0/1:5,2:7:69:69,0,253 chr1 185795 . G T 40.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.75;ClippingRankSum=-5.500e-01;DP=7;ExcessHet=3.0103;FS=8.451;MLEAC=1;MLEAF=0.500;MQ=22.46;MQRankSum=1.75;QD=5.82;ReadPosRankSum=1.75;SOR=0.829;VQSLOD=-4.011e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:4,3:7:69:69,0,78 chr1 186209 . T C 230.78 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.07;QD=25.64;SOR=4.615;VQSLOD=-2.672e+00;culprit=QD GT:AD:DP:GQ:PL 1/1:0,9:9:27:259,27,0 chr1 186536 . C T 459.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.099;ClippingRankSum=1.20;DP=39;ExcessHet=3.0103;FS=4.763;MLEAC=1;MLEAF=0.500;MQ=35.32;MQRankSum=0.836;NEGATIVE_TRAIN_SITE;QD=11.79;ReadPosRankSum=1.52;SOR=0.552;VQSLOD=-2.449e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:17,22:39:99:488,0,386 chr1 186810 . C G 186.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.755;ClippingRankSum=0.044;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.20;MQRankSum=2.98;NEGATIVE_TRAIN_SITE;QD=10.38;ReadPosRankSum=-5.780e-01;SOR=0.859;VQSLOD=-2.060e-02;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:10,8:18:99:215,0,252 chr1 186835 . A G 650.77 PASS AC=2;AF=1.00;AN=2;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=35.17;QD=30.99;SOR=2.200;VQSLOD=2.09;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,21:21:63:679,63,0 chr1 187019 . G A 851.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=1.43;ClippingRankSum=0.320;DP=44;ExcessHet=3.0103;FS=1.490;MLEAC=1;MLEAF=0.500;MQ=38.65;MQRankSum=-4.568e+00;NEGATIVE_TRAIN_SITE;QD=19.36;ReadPosRankSum=0.00;SOR=0.373;VQSLOD=-2.484e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:9,35:44:99:880,0,147 chr1 187102 . C G 38.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.196e+00;ClippingRankSum=-1.061e+00;DP=48;ExcessHet=3.0103;FS=1.663;MLEAC=1;MLEAF=0.500;MQ=37.49;MQRankSum=2.79;NEGATIVE_TRAIN_SITE;QD=0.82;ReadPosRankSum=-3.140e-01;SOR=1.316;VQSLOD=-4.162e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:40,7:47:67:67,0,1018 chr1 187302 . A G 84.03 PASS AC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.26;QD=21.01;SOR=1.609;VQSLOD=-4.745e-01;culprit=QD GT:AD:DP:GQ:PL 1/1:0,4:4:12:112,12,0 chr1 187485 . G A 572.77 VQSRTrancheSNP99.95to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=1.00;ClippingRankSum=0.639;DP=19;ExcessHet=3.0103;FS=6.767;MLEAC=2;MLEAF=1.00;MQ=23.12;MQRankSum=1.55;QD=30.15;ReadPosRankSum=1.55;SOR=2.788;VQSLOD=-5.027e+00;culprit=SOR GT:AD:DP:GQ:PGT:PID:PL 1/1:1,18:19:32:1|1:187485_G_A:601,32,0 chr1 187497 . G A 138.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=3.34;ClippingRankSum=-5.370e-01;DP=19;ExcessHet=3.0103;FS=6.419;MLEAC=1;MLEAF=0.500;MQ=23.27;MQRankSum=0.454;QD=7.30;ReadPosRankSum=0.950;SOR=2.833;VQSLOD=-3.595e+00;culprit=SOR GT:AD:DP:GQ:PGT:PID:PL 0/1:11,8:19:99:0|1:187485_G_A:167,0,227 chr1 187744 . A G 220.74 VQSRTrancheSNP99.95to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=-7.910e-01;ClippingRankSum=0.158;DP=11;ExcessHet=3.0103;FS=10.414;MLEAC=2;MLEAF=1.00;MQ=22.91;MQRankSum=1.42;QD=20.07;ReadPosRankSum=-1.580e-01;SOR=4.798;VQSLOD=-5.788e+00;culprit=SOR GT:AD:DP:GQ:PL 1/1:1,10:11:6:248,6,0 chr1 189234 . C T 198.82 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.180e-01;ClippingRankSum=-1.180e-01;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.94;MQRankSum=1.53;QD=18.07;ReadPosRankSum=-1.180e-01;SOR=2.494;VQSLOD=-3.975e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:2,9:11:19:227,0,19 chr1 189269 . T A 420.77 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.84;QD=28.05;SOR=5.549;VQSLOD=-2.691e+00;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,15:15:45:449,45,0 chr1 189392 . ACC A 872.73 PASS AC=2;AF=1.00;AN=2;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.88;QD=30.83;SOR=0.990;VQSLOD=5.74;culprit=FS GT:AD:DP:GQ:PL 1/1:0,21:21:63:910,63,0 chr1 189771 . T C 242.78 PASS AC=2;AF=1.00;AN=2;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.61;QD=30.35;SOR=1.179;VQSLOD=2.23;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,8:8:24:1|1:189771_T_C:271,24,0 chr1 189772 . G A 37.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.572;ClippingRankSum=0.572;DP=8;ExcessHet=3.0103;FS=3.332;MLEAC=1;MLEAF=0.500;MQ=29.61;MQRankSum=0.00;QD=4.72;ReadPosRankSum=0.572;SOR=2.303;VQSLOD=-2.747e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:6,2:8:66:0|1:189771_T_C:66,0,246 chr1 189777 . G C 34.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-6.700e-02;ClippingRankSum=1.18;DP=9;ExcessHet=3.0103;FS=3.522;MLEAC=1;MLEAF=0.500;MQ=30.93;MQRankSum=-6.700e-02;NEGATIVE_TRAIN_SITE;QD=3.86;ReadPosRankSum=1.18;SOR=2.266;VQSLOD=-2.603e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:7,2:9:63:0|1:189771_T_C:63,0,275 chr1 189811 . C A 166.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.103;ClippingRankSum=-1.098e+00;DP=10;ExcessHet=3.0103;FS=2.808;MLEAC=1;MLEAF=0.500;MQ=30.44;MQRankSum=0.851;QD=16.68;ReadPosRankSum=0.851;SOR=1.919;VQSLOD=-2.826e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:5,5:10:99:0|1:189771_T_C:195,0,161 chr1 189829 . T A 172.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=0.684;ClippingRankSum=0.322;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.96;MQRankSum=0.684;QD=21.60;ReadPosRankSum=1.52;SOR=1.329;VQSLOD=-1.067e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:3,5:8:99:0|1:189771_T_C:201,0,106 chr1 190311 . C T 136.74 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-7.420e-01;ClippingRankSum=0.742;DP=7;ExcessHet=3.0103;FS=8.451;MLEAC=1;MLEAF=0.500;MQ=30.92;MQRankSum=0.742;NEGATIVE_TRAIN_SITE;QD=19.53;ReadPosRankSum=-7.420e-01;SOR=3.897;VQSLOD=-4.058e+00;culprit=SOR GT:AD:DP:GQ:PL 0/1:1,6:7:6:164,0,6 chr1 190659 . T C 112.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.365;ClippingRankSum=-3.650e-01;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.96;MQRankSum=1.13;QD=11.28;ReadPosRankSum=-3.650e-01;SOR=1.179;VQSLOD=0.521;culprit=MQ GT:AD:DP:GQ:PL 0/1:4,6:10:94:141,0,94 chr1 190768 . G A 343.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.510;ClippingRankSum=0.962;DP=17;ExcessHet=3.0103;FS=2.694;MLEAC=1;MLEAF=0.500;MQ=51.84;MQRankSum=1.19;NEGATIVE_TRAIN_SITE;QD=20.22;ReadPosRankSum=0.283;SOR=2.147;VQSLOD=-1.544e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:4,13:17:75:372,0,75 chr1 191910 . C T 92.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.210e-01;ClippingRankSum=0.609;DP=18;ExcessHet=3.0103;FS=13.667;MLEAC=1;MLEAF=0.500;MQ=28.85;MQRankSum=-5.150e-01;QD=5.15;ReadPosRankSum=-7.960e-01;SOR=2.215;VQSLOD=-3.168e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:12,6:18:99:121,0,286 chr1 191944 . G A 356.82 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;BaseQRankSum=-2.170e-01;ClippingRankSum=0.00;DP=16;ExcessHet=3.0103;FS=3.590;MLEAC=2;MLEAF=1.00;MQ=27.82;MQRankSum=1.52;QD=22.30;ReadPosRankSum=0.00;SOR=0.829;VQSLOD=-2.768e+00;culprit=QD GT:AD:DP:GQ:PL 1/1:1,15:16:19:385,19,0 chr1 192025 . G A 166.80 PASS AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=23.83;SOR=4.174;VQSLOD=-1.205e-01;culprit=QD GT:AD:DP:GQ:PL 1/1:0,7:7:21:195,21,0 chr1 198894 . G A 44.74 PASS AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.00;NEGATIVE_TRAIN_SITE;QD=22.37;SOR=2.303;VQSLOD=-1.870e-02;culprit=QD GT:AD:DP:GQ:PL 1/1:0,2:2:6:72,6,0 chr1 199076 . C T 62.74 PASS AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=31.37;SOR=2.303;VQSLOD=0.665;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:199076_C_T:90,6,0 chr1 199081 . A G 62.74 PASS AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=31.37;SOR=2.303;VQSLOD=1.44;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:199076_C_T:90,6,0 chr1 199092 . A C 107.28 PASS AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=29.67;SOR=2.833;VQSLOD=0.521;culprit=SOR GT:AD:DP:GQ:PGT:PID:PL 1/1:0,3:3:9:1|1:199076_C_T:135,9,0 chr1 199107 . G T 107.28 PASS AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.00;QD=34.04;SOR=2.833;VQSLOD=0.205;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,3:3:9:1|1:199076_C_T:135,9,0 chr1 202007 . G A 214.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=2.05;ClippingRankSum=-5.730e-01;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.73;MQRankSum=0.248;NEGATIVE_TRAIN_SITE;QD=23.86;ReadPosRankSum=0.573;SOR=1.402;VQSLOD=-1.041e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:3,6:9:99:0|1:202007_G_A:243,0,108 chr1 202016 . C T 334.78 VQSRTrancheSNP99.80to99.90 AC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=31.73;NEGATIVE_TRAIN_SITE;QD=32.42;SOR=4.615;VQSLOD=-1.559e+00;culprit=QD GT:AD:DP:GQ:PL 1/1:0,9:9:27:363,27,0 chr1 202029 . A G 211.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.650e-01;ClippingRankSum=-6.330e-01;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.65;MQRankSum=0.741;NEGATIVE_TRAIN_SITE;QD=21.18;ReadPosRankSum=1.13;SOR=1.085;VQSLOD=0.316;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:4,6:10:99:0|1:202007_G_A:240,0,150 chr1 202031 . A G 211.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-6.330e-01;ClippingRankSum=0.365;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.65;MQRankSum=-6.330e-01;NEGATIVE_TRAIN_SITE;QD=21.18;ReadPosRankSum=1.13;SOR=1.085;VQSLOD=0.464;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:4,6:10:99:0|1:202007_G_A:240,0,150 chr1 202075 . AAAAAT A 37.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.231e+00;ClippingRankSum=0.358;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.53;MQRankSum=-1.231e+00;QD=7.55;ReadPosRankSum=-3.580e-01;SOR=0.446;VQSLOD=2.35;culprit=FS GT:AD:DP:GQ:PL 0/1:3,2:5:75:75,0,120 chr1 202170 . C T 38.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.48;ClippingRankSum=0.185;DP=12;ExcessHet=3.0103;FS=13.424;MLEAC=1;MLEAF=0.500;MQ=42.03;MQRankSum=-1.479e+00;NEGATIVE_TRAIN_SITE;QD=3.23;ReadPosRankSum=-7.400e-01;SOR=2.781;VQSLOD=-1.573e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:9,3:12:67:67,0,177 chr1 202217 . G A 75.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=2.64;ClippingRankSum=-1.599e+00;DP=12;ExcessHet=3.0103;FS=15.185;MLEAC=1;MLEAF=0.500;MQ=42.79;MQRankSum=-1.239e+00;NEGATIVE_TRAIN_SITE;QD=6.31;ReadPosRankSum=-8.250e-01;SOR=3.226;VQSLOD=-1.629e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:8,4:12:99:104,0,195 chr1 202259 . G T 110.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-6.500e-02;ClippingRankSum=-4.520e-01;DP=14;ExcessHet=3.0103;FS=9.890;MLEAC=1;MLEAF=0.500;MQ=42.48;MQRankSum=-1.872e+00;NEGATIVE_TRAIN_SITE;QD=7.91;ReadPosRankSum=1.36;SOR=2.217;VQSLOD=-1.180e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:8,6:14:99:139,0,188 chr1 202312 . G A 63.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.11;ClippingRankSum=-5.660e-01;DP=11;ExcessHet=3.0103;FS=6.264;MLEAC=1;MLEAF=0.500;MQ=39.25;MQRankSum=-1.931e+00;NEGATIVE_TRAIN_SITE;QD=5.80;ReadPosRankSum=0.566;SOR=2.833;VQSLOD=-1.566e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:8,3:11:92:0|1:202312_G_A:92,0,257 chr1 202496 . T A 32.74 VQSRTrancheSNP99.95to100.00 AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.08;QD=16.37;SOR=2.303;VQSLOD=-3.288e+00;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:60,6,0 chr1 205748 . G C 34.74 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=32.28;NEGATIVE_TRAIN_SITE;QD=17.37;SOR=2.303;VQSLOD=-2.397e+00;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:62,6,0 chr1 261454 rs10047119 T A 79.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.20;ClippingRankSum=-1.203e+00;DB;DP=9;ExcessHet=3.0103;FS=3.332;MLEAC=1;MLEAF=0.500;MQ=21.78;MQRankSum=1.42;QD=8.86;ReadPosRankSum=-5.730e-01;SOR=2.833;VQSLOD=-4.142e+00;culprit=SOR GT:AD:DP:GQ:PGT:PID:PL 0/1:6,3:9:99:0|1:261454_T_A:108,0,277 chr1 261463 rs10047174 C A 79.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.20;ClippingRankSum=-2.480e-01;DB;DP=9;ExcessHet=3.0103;FS=3.332;MLEAC=1;MLEAF=0.500;MQ=21.78;MQRankSum=2.05;QD=8.86;ReadPosRankSum=0.248;SOR=2.833;VQSLOD=-4.229e+00;culprit=SOR GT:AD:DP:GQ:PGT:PID:PL 0/1:6,3:9:99:0|1:261454_T_A:108,0,277 chr1 261478 rs10047175 C A 45.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.03;ClippingRankSum=1.66;DB;DP=11;ExcessHet=3.0103;FS=6.264;MLEAC=1;MLEAF=0.500;MQ=21.82;MQRankSum=0.678;QD=4.16;ReadPosRankSum=-2.780e-01;SOR=2.833;VQSLOD=-3.879e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:7,4:11:74:74,0,152 chr1 261495 rs10047121 T C 86.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-7.660e-01;ClippingRankSum=2.18;DB;DP=15;ExcessHet=3.0103;FS=6.410;MLEAC=1;MLEAF=0.500;MQ=21.87;MQRankSum=0.884;QD=5.78;ReadPosRankSum=0.177;SOR=2.833;VQSLOD=-3.821e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:9,6:15:99:115,0,194 chr1 261729 rs200482415 G C 115.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.361e+00;ClippingRankSum=-4.830e-01;DB;DP=73;ExcessHet=3.0103;FS=8.738;MLEAC=1;MLEAF=0.500;MQ=26.48;MQRankSum=-1.843e+00;QD=1.59;ReadPosRankSum=0.946;SOR=2.012;VQSLOD=-7.914e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:59,14:73:99:144,0,1335 chr1 261753 rs10047230 G A 498.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.54;ClippingRankSum=0.176;DB;DP=78;ExcessHet=3.0103;FS=7.913;MLEAC=1;MLEAF=0.500;MQ=26.52;MQRankSum=-2.070e-01;QD=6.39;ReadPosRankSum=-5.070e-01;SOR=0.878;VQSLOD=-8.323e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:49,29:78:99:527,0,1060 chr1 261775 rs112821789 C T 167.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.420;ClippingRankSum=0.071;DB;DP=76;ExcessHet=3.0103;FS=10.444;MLEAC=1;MLEAF=0.500;MQ=26.91;MQRankSum=-7.050e-01;QD=2.24;ReadPosRankSum=1.24;SOR=1.516;VQSLOD=-8.489e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:59,16:75:99:196,0,1312 chr1 263722 rs112455420 C G 118.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.122e+00;ClippingRankSum=-1.220e+00;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=38.45;MQRankSum=1.12;POSITIVE_TRAIN_SITE;QD=6.99;ReadPosRankSum=0.927;SOR=0.941;VQSLOD=2.47;culprit=QD GT:AD:DP:GQ:PL 0/1:10,7:17:99:147,0,286 chr1 264557 rs200066978 A G 37.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.16;ClippingRankSum=-7.280e-01;DB;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.17;MQRankSum=-2.055e+00;NEGATIVE_TRAIN_SITE;QD=0.63;ReadPosRankSum=0.881;SOR=0.576;VQSLOD=-4.535e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:52,8:60:66:66,0,1422 chr1 264562 rs8179466 C T 30.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.42;ClippingRankSum=-1.780e-01;DB;DP=62;ExcessHet=3.0103;FS=3.427;MLEAC=1;MLEAF=0.500;MQ=40.79;MQRankSum=-1.270e+00;NEGATIVE_TRAIN_SITE;QD=0.50;ReadPosRankSum=-1.360e-01;SOR=0.269;VQSLOD=-5.105e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:54,8:62:59:59,0,1592 chr1 264627 rs200864529 A G 1012.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.544e+00;ClippingRankSum=-5.190e-01;DB;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=42.21;MQRankSum=3.16;NEGATIVE_TRAIN_SITE;QD=12.98;ReadPosRankSum=0.791;SOR=0.669;VQSLOD=-6.961e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:34,44:78:99:1041,0,774 chr1 264681 rs8179455 A G 194.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.679e+00;ClippingRankSum=0.378;DB;DP=62;ExcessHet=3.0103;FS=2.473;MLEAC=1;MLEAF=0.500;MQ=44.44;MQRankSum=-5.043e+00;NEGATIVE_TRAIN_SITE;QD=3.14;ReadPosRankSum=-8.800e-02;SOR=0.824;VQSLOD=-4.360e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:46,16:62:99:223,0,1281 chr1 264730 rs8179403 T A 973.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.540e-01;ClippingRankSum=-1.858e+00;DB;DP=50;ExcessHet=3.0103;FS=2.946;MLEAC=1;MLEAF=0.500;MQ=42.06;MQRankSum=-1.371e+00;NEGATIVE_TRAIN_SITE;QD=19.48;ReadPosRankSum=-7.740e-01;SOR=0.352;VQSLOD=-2.673e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:13,37:50:99:1002,0,260 chr1 264858 rs201234721 T C 442.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=2.72;ClippingRankSum=0.198;DB;DP=34;ExcessHet=3.0103;FS=9.298;MLEAC=1;MLEAF=0.500;MQ=36.06;MQRankSum=1.42;NEGATIVE_TRAIN_SITE;QD=13.42;ReadPosRankSum=-4.140e-01;SOR=2.527;VQSLOD=-2.508e+00;culprit=SOR GT:AD:DP:GQ:PL 0/1:16,17:33:99:471,0,354 chr1 266093 rs6603780 C G 745.77 VQSRTrancheSNP99.60to99.80 AC=2;AF=1.00;AN=2;BaseQRankSum=-6.000e-02;ClippingRankSum=-5.380e-01;DB;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.96;MQRankSum=1.61;QD=25.72;ReadPosRankSum=0.657;SOR=0.356;VQSLOD=-7.938e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:1,28:29:59:1|1:266086_C_T:774,59,0 chr1 266225 rs6422503 C A 978.77 PASS AC=2;AF=1.00;AN=2;DB;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.15;QD=27.96;SOR=0.749;VQSLOD=-2.728e-01;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,35:35:99:1007,105,0 chr1 266970 . C T 55.28 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.00;QD=18.43;SOR=2.833;VQSLOD=-2.827e+00;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,3:3:9:83,9,0 chr1 267521 rs62635272 T A 41.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.697;ClippingRankSum=-4.900e-02;DB;DP=63;ExcessHet=3.0103;FS=15.529;MLEAC=1;MLEAF=0.500;MQ=29.88;MQRankSum=-7.370e-01;QD=0.66;ReadPosRankSum=3.11;SOR=3.045;VQSLOD=-7.135e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:54,9:63:70:70,0,1398 chr1 267739 rs184796003 C A 126.77 VQSRTrancheSNP99.50to99.60 AC=1;AF=0.500;AN=2;BaseQRankSum=2.59;ClippingRankSum=-1.311e+00;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.21;MQRankSum=-4.370e-01;QD=5.07;ReadPosRankSum=-2.900e-02;SOR=0.327;VQSLOD=-6.767e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:17,8:25:99:155,0,405 chr1 267777 rs768683158 C CAAAA 103.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.540;ClippingRankSum=-1.003e+00;DB;DP=17;ExcessHet=3.0103;FS=3.041;MLEAC=1;MLEAF=0.500;MQ=31.01;MQRankSum=2.24;NEGATIVE_TRAIN_SITE;QD=7.98;ReadPosRankSum=0.386;SOR=2.215;VQSLOD=-6.353e-01;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:9,4:13:99:141,0,366 chr1 268012 rs112186068 G A 227.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.651e+00;ClippingRankSum=0.664;DB;DP=75;ExcessHet=3.0103;FS=1.085;MLEAC=1;MLEAF=0.500;MQ=46.06;MQRankSum=-1.209e+00;NEGATIVE_TRAIN_SITE;QD=3.04;ReadPosRankSum=-1.284e+00;SOR=0.491;VQSLOD=-6.638e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:58,17:75:99:256,0,1633 chr1 268130 rs6603779 G T 772.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=1.32;ClippingRankSum=-1.730e-01;DB;DP=42;ExcessHet=3.0103;FS=9.664;MLEAC=1;MLEAF=0.500;MQ=45.32;MQRankSum=-4.736e+00;NEGATIVE_TRAIN_SITE;QD=18.40;ReadPosRankSum=-8.140e-01;SOR=0.651;VQSLOD=-2.279e+00;culprit=MQRankSum GT:AD:DP:GQ:PGT:PID:PL 0/1:14,28:42:99:0|1:268121_G_C:801,0,345 chr1 268516 rs6670732 C T 636.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=2.12;ClippingRankSum=-9.540e-01;DB;DP=66;ExcessHet=3.0103;FS=0.987;MLEAC=1;MLEAF=0.500;MQ=49.00;MQRankSum=-2.978e+00;NEGATIVE_TRAIN_SITE;QD=9.65;ReadPosRankSum=0.344;SOR=0.502;VQSLOD=-4.306e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:38,28:66:99:665,0,1002 chr1 268559 rs8179401 A C 1168.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.166e+00;ClippingRankSum=-6.370e-01;DB;DP=63;ExcessHet=3.0103;FS=1.189;MLEAC=1;MLEAF=0.500;MQ=45.97;MQRankSum=-5.001e+00;NEGATIVE_TRAIN_SITE;QD=18.55;ReadPosRankSum=-9.100e-02;SOR=0.428;VQSLOD=-4.053e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:14,49:63:99:1197,0,263 chr1 268716 . T C 60.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.275e+00;ClippingRankSum=1.43;DP=28;ExcessHet=3.0103;FS=2.758;MLEAC=1;MLEAF=0.500;MQ=34.61;MQRankSum=0.532;NEGATIVE_TRAIN_SITE;QD=2.17;ReadPosRankSum=0.812;SOR=0.169;VQSLOD=-2.634e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:22,6:28:89:89,0,615 chr1 269191 . G C 67.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-5.270e-01;ClippingRankSum=-6.400e-01;DP=38;ExcessHet=3.0103;FS=1.632;MLEAC=1;MLEAF=0.500;MQ=41.93;MQRankSum=-5.650e-01;NEGATIVE_TRAIN_SITE;QD=1.78;ReadPosRankSum=2.26;SOR=0.814;VQSLOD=-2.399e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:31,7:38:96:96,0,797 chr1 269413 rs199966892 G A 489.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.904;ClippingRankSum=1.49;DB;DP=37;ExcessHet=3.0103;FS=1.257;MLEAC=1;MLEAF=0.500;MQ=48.33;MQRankSum=1.43;NEGATIVE_TRAIN_SITE;QD=13.24;ReadPosRankSum=1.03;SOR=0.936;VQSLOD=-1.671e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:16,21:37:99:518,0,370 chr1 269588 rs184451216 A G 40.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.150e+00;ClippingRankSum=-5.500e-01;DB;DP=19;ExcessHet=3.0103;FS=10.620;MLEAC=1;MLEAF=0.500;MQ=35.66;MQRankSum=0.050;NEGATIVE_TRAIN_SITE;QD=2.15;ReadPosRankSum=-1.250e+00;SOR=3.238;VQSLOD=-2.435e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:15,4:19:69:69,0,395 chr1 269731 rs201702841 G T 85.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.453;ClippingRankSum=1.25;DB;DP=16;ExcessHet=3.0103;FS=2.663;MLEAC=1;MLEAF=0.500;MQ=28.48;MQRankSum=1.70;QD=5.36;ReadPosRankSum=-6.800e-01;SOR=1.445;VQSLOD=-2.914e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:11,5:16:99:114,0,243 chr1 269781 rs200000439 C T 116.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=1.75;ClippingRankSum=-1.408e+00;DB;DP=11;ExcessHet=3.0103;FS=2.632;MLEAC=1;MLEAF=0.500;MQ=25.19;MQRankSum=-4.660e-01;QD=10.62;ReadPosRankSum=0.717;SOR=1.802;VQSLOD=-3.022e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:5,6:11:99:145,0,118 chr1 270396 rs202156508 C T 229.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.130e-01;ClippingRankSum=0.227;DB;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.13;MQRankSum=-1.246e+00;QD=14.36;ReadPosRankSum=1.36;SOR=1.609;VQSLOD=-1.544e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:5,11:16:99:258,0,101 chr1 270684 rs143434963 C G 250.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=2.27;ClippingRankSum=0.123;DB;DP=62;ExcessHet=3.0103;FS=1.165;MLEAC=1;MLEAF=0.500;MQ=34.22;MQRankSum=-1.107e+00;NEGATIVE_TRAIN_SITE;QD=4.11;ReadPosRankSum=0.894;SOR=1.044;VQSLOD=-5.056e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:45,16:61:99:279,0,1147 chr1 271147 rs147990930 T G 266.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.189e+00;ClippingRankSum=0.849;DB;DP=17;ExcessHet=3.0103;FS=9.187;MLEAC=1;MLEAF=0.500;MQ=23.70;MQRankSum=0.283;QD=15.69;ReadPosRankSum=-1.076e+00;SOR=3.767;VQSLOD=-4.300e+00;culprit=SOR GT:AD:DP:GQ:PL 0/1:4,13:17:49:295,0,49 chr1 271569 rs79974410 A G 229.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.489;ClippingRankSum=0.133;DB;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=46.06;MQRankSum=-3.599e+00;QD=12.76;ReadPosRankSum=-4.890e-01;SOR=0.693;VQSLOD=1.55;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:8,10:18:99:258,0,131 chr1 271618 rs11490246 C T 254.78 PASS AC=2;AF=1.00;AN=2;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.79;POSITIVE_TRAIN_SITE;QD=28.31;SOR=0.892;VQSLOD=5.40;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,9:9:27:283,27,0 chr1 272378 rs201921502 A T 108.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.825;ClippingRankSum=0.825;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.79;MQRankSum=-3.870e-01;QD=9.89;ReadPosRankSum=1.19;SOR=0.223;VQSLOD=-5.192e-01;culprit=MQ GT:AD:DP:GQ:PL 0/1:5,6:11:99:137,0,106 chr1 272389 rs200295906 C T 69.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-7.290e-01;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.06;MQRankSum=-1.159e+00;QD=7.75;ReadPosRankSum=0.876;SOR=0.223;VQSLOD=-9.455e-01;culprit=MQ GT:AD:DP:GQ:PL 0/1:4,5:9:84:98,0,84 chr1 274015 rs62635275 A G 128.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.50;ClippingRankSum=0.887;DB;DP=20;ExcessHet=3.0103;FS=1.885;MLEAC=1;MLEAF=0.500;MQ=48.68;MQRankSum=-3.742e+00;NEGATIVE_TRAIN_SITE;QD=6.44;ReadPosRankSum=0.039;SOR=0.269;VQSLOD=-1.537e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:12,8:20:99:157,0,307 chr1 274099 rs140116466 CAAGT C 679.73 VQSRTrancheINDEL99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.541e+00;ClippingRankSum=0.861;DB;DP=33;ExcessHet=3.0103;FS=11.357;MLEAC=1;MLEAF=0.500;MQ=42.97;MQRankSum=-3.223e+00;NEGATIVE_TRAIN_SITE;QD=21.93;ReadPosRankSum=0.953;SOR=1.308;VQSLOD=-2.958e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:13,18:31:99:717,0,656 chr1 274537 rs796211217 A G 82.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.532e+00;ClippingRankSum=1.19;DB;DP=11;ExcessHet=3.0103;FS=6.154;MLEAC=1;MLEAF=0.500;MQ=25.49;MQRankSum=-4.660e-01;QD=7.52;ReadPosRankSum=1.19;SOR=1.889;VQSLOD=-2.997e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:6,5:11:99:111,0,141 chr1 274895 rs796317578 C T 30.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;ClippingRankSum=0.248;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.13;MQRankSum=1.20;QD=3.42;ReadPosRankSum=-1.203e+00;SOR=0.593;VQSLOD=-1.202e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:6,3:9:59:59,0,124 chr1 275273 rs112390583 C A 67.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-8.210e-01;ClippingRankSum=1.06;DB;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.05;MQRankSum=-4.030e-01;QD=1.58;ReadPosRankSum=1.63;SOR=0.653;VQSLOD=-2.791e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:34,9:43:96:96,0,806 chr1 275337 rs199660279 T C 71.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.226;ClippingRankSum=0.609;DB;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.56;MQRankSum=-2.069e+00;QD=1.84;ReadPosRankSum=0.191;SOR=0.859;VQSLOD=-2.630e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:31,8:39:99:100,0,781 chr1 275388 rs202020431 G A 97.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.858;ClippingRankSum=-9.130e-01;DB;DP=27;ExcessHet=3.0103;FS=1.983;MLEAC=1;MLEAF=0.500;MQ=27.49;MQRankSum=0.526;QD=3.62;ReadPosRankSum=0.083;SOR=1.300;VQSLOD=-3.074e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:20,7:27:99:126,0,463 chr1 275505 rs200930606 AG A 44.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;ClippingRankSum=0.667;DB;DP=16;ExcessHet=3.0103;FS=6.317;MLEAC=1;MLEAF=0.500;MQ=32.39;MQRankSum=-1.152e+00;NEGATIVE_TRAIN_SITE;QD=2.80;ReadPosRankSum=1.40;SOR=3.258;VQSLOD=-8.009e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:12,4:16:82:82,0,365 chr1 275583 rs768053647 TTTTA T 130.73 PASS AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.63;QD=37.76;SOR=1.609;VQSLOD=3.90;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:4:6:90,6,0 chr1 275616 . T C 46.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.23;ClippingRankSum=-1.231e+00;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=48.58;MQRankSum=-3.580e-01;QD=9.35;ReadPosRankSum=1.23;SOR=0.368;VQSLOD=1.65;culprit=MQ GT:AD:DP:GQ:PL 0/1:3,2:5:75:75,0,100 chr1 277226 rs62635277 A C 202.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.606e+00;ClippingRankSum=2.11;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.49;MQRankSum=-1.099e+00;QD=15.60;ReadPosRankSum=0.085;SOR=2.147;VQSLOD=-3.773e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:3,10:13:44:231,0,44 chr1 277677 rs62639107 G T 779.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=2.11;ClippingRankSum=-3.990e-01;DB;DP=42;ExcessHet=3.0103;FS=3.097;MLEAC=1;MLEAF=0.500;MQ=42.57;MQRankSum=0.044;NEGATIVE_TRAIN_SITE;QD=18.57;ReadPosRankSum=2.08;SOR=0.337;VQSLOD=-1.992e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:10,32:42:99:808,0,130 chr1 277801 rs376115996 G A 63.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=1.82;ClippingRankSum=-1.530e-01;DB;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=35.70;MQRankSum=0.766;NEGATIVE_TRAIN_SITE;QD=1.82;ReadPosRankSum=0.635;SOR=0.382;VQSLOD=-9.187e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:29,6:35:92:92,0,821 chr1 277834 rs62639108 G A 375.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.830;ClippingRankSum=0.747;DB;DP=30;ExcessHet=3.0103;FS=18.479;MLEAC=1;MLEAF=0.500;MQ=35.94;MQRankSum=1.08;NEGATIVE_TRAIN_SITE;QD=12.53;ReadPosRankSum=0.290;SOR=4.044;VQSLOD=-3.247e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:15,15:30:99:404,0,342 chr1 278165 rs202029170 CAGG C 231.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.067;ClippingRankSum=1.18;DB;DP=10;ExcessHet=3.0103;FS=3.522;MLEAC=1;MLEAF=0.500;MQ=45.73;MQRankSum=1.18;NEGATIVE_TRAIN_SITE;QD=25.75;ReadPosRankSum=-7.620e-01;SOR=0.515;VQSLOD=-5.020e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:2,7:9:63:269,0,63 chr1 278240 . CAA C 89.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-7.200e-01;ClippingRankSum=-1.380e+00;DP=8;ExcessHet=3.0103;FS=11.761;MLEAC=1;MLEAF=0.500;MQ=35.73;MQRankSum=-7.200e-01;NEGATIVE_TRAIN_SITE;QD=14.96;ReadPosRankSum=0.00;SOR=3.223;VQSLOD=-9.352e-01;culprit=SOR GT:AD:DP:GQ:PL 0/1:2,4:6:52:127,0,52 chr1 278553 rs375277195 G C 62.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.87;ClippingRankSum=-1.447e+00;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.61;MQRankSum=-6.330e-01;QD=6.28;ReadPosRankSum=0.00;SOR=0.412;VQSLOD=0.974;culprit=QD GT:AD:DP:GQ:PL 0/1:6,4:10:91:91,0,158 chr1 279951 rs62639110 G A 154.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=0.264;ClippingRankSum=0.551;DB;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=24.99;MQRankSum=1.65;QD=5.53;ReadPosRankSum=-7.430e-01;SOR=0.446;VQSLOD=-1.038e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:18,10:28:99:183,0,434 chr1 280592 . T C 186.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-8.690e-01;ClippingRankSum=-4.670e-01;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.76;MQRankSum=0.869;NEGATIVE_TRAIN_SITE;QD=15.56;ReadPosRankSum=-2.590e-01;SOR=1.863;VQSLOD=-2.065e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:6,6:12:99:0|1:280592_T_C:215,0,345 chr1 280599 rs372766634 T C 186.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.843e+00;ClippingRankSum=-8.690e-01;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.76;MQRankSum=0.869;NEGATIVE_TRAIN_SITE;QD=15.56;ReadPosRankSum=-1.073e+00;SOR=1.863;VQSLOD=-2.419e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:6,6:12:99:0|1:280592_T_C:215,0,345 chr1 282607 rs11489922 G A 35.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-5.500e-01;ClippingRankSum=0.937;DB;DP=7;ExcessHet=3.0103;FS=8.451;MLEAC=1;MLEAF=0.500;MQ=24.44;MQRankSum=-1.754e+00;QD=5.11;ReadPosRankSum=0.550;SOR=2.788;VQSLOD=-3.392e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:4,3:7:64:64,0,98 chr1 282616 . G GA 42.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-5.500e-01;DP=7;ExcessHet=3.0103;FS=8.451;MLEAC=1;MLEAF=0.500;MQ=24.44;MQRankSum=-1.754e+00;NEGATIVE_TRAIN_SITE;QD=6.10;ReadPosRankSum=0.550;SOR=2.788;VQSLOD=-1.582e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:4,3:7:80:80,0,117 chr1 282888 rs200683317 A G 39.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.412e+00;ClippingRankSum=-1.420e-01;DB;DP=24;ExcessHet=3.0103;FS=2.644;MLEAC=1;MLEAF=0.500;MQ=33.40;MQRankSum=-1.208e+00;NEGATIVE_TRAIN_SITE;QD=1.66;ReadPosRankSum=-1.137e+00;SOR=1.508;VQSLOD=-2.330e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:19,5:24:68:68,0,555 chr1 283205 rs200725328 T C 77.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.940;ClippingRankSum=-3.920e-01;DB;DP=22;ExcessHet=3.0103;FS=12.704;MLEAC=1;MLEAF=0.500;MQ=33.94;MQRankSum=0.783;NEGATIVE_TRAIN_SITE;QD=3.53;ReadPosRankSum=-5.480e-01;SOR=3.606;VQSLOD=-2.837e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:17,5:22:99:106,0,416 chr1 283477 rs62639117 G A 166.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.470;ClippingRankSum=1.67;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.92;MQRankSum=-2.148e+00;QD=16.68;ReadPosRankSum=0.336;SOR=0.693;VQSLOD=-4.840e-02;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:5,5:10:99:0|1:283477_G_A:195,0,260 chr1 283492 rs767396087 ACT A 199.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.650e-01;ClippingRankSum=0.00;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=22.92;MQRankSum=-1.447e+00;QD=19.97;ReadPosRankSum=0.741;SOR=1.085;VQSLOD=2.94;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 0/1:4,6:10:99:0|1:283477_G_A:237,0,232 chr1 284929 rs62639119 A G 240.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.359e+00;ClippingRankSum=0.103;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=31.46;MQRankSum=-1.692e+00;NEGATIVE_TRAIN_SITE;QD=9.26;ReadPosRankSum=0.718;SOR=1.002;VQSLOD=0.364;culprit=MQ GT:AD:DP:GQ:PL 0/1:13,13:26:99:269,0,322 chr1 285104 . C A 30.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;ClippingRankSum=0.248;DP=9;ExcessHet=3.0103;FS=13.222;MLEAC=1;MLEAF=0.500;MQ=34.57;MQRankSum=-1.683e+00;NEGATIVE_TRAIN_SITE;QD=3.42;ReadPosRankSum=-5.730e-01;SOR=2.780;VQSLOD=-2.411e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:6,3:9:59:59,0,113 chr1 285345 . C T 51.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=2.35;ClippingRankSum=-1.230e+00;DP=23;ExcessHet=3.0103;FS=13.397;MLEAC=1;MLEAF=0.500;MQ=32.36;MQRankSum=-1.677e+00;NEGATIVE_TRAIN_SITE;QD=2.25;ReadPosRankSum=1.23;SOR=3.602;VQSLOD=-3.050e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:18,5:23:80:80,0,412 chr1 285441 rs201544877 C T 134.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.99;ClippingRankSum=-7.600e-01;DB;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=27.33;MQRankSum=-6.880e-01;QD=6.42;ReadPosRankSum=0.398;SOR=0.446;VQSLOD=0.569;culprit=MQ GT:AD:DP:GQ:PL 0/1:13,8:21:99:163,0,276 chr1 286158 rs200542524 A ATG 209.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.05;QD=29.97;SOR=1.609;VQSLOD=4.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,7:7:21:247,21,0 chr1 286272 rs554693544 A G 98.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=32.98;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=24.51;SOR=3.258;VQSLOD=1.18;culprit=QD GT:AD:DP:GQ:PL 1/1:0,4:4:12:126,12,0 chr1 287171 rs377659925 T A 65.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=30.56;QD=21.76;SOR=1.179;VQSLOD=0.076;culprit=QD GT:AD:DP:GQ:PL 1/1:0,3:3:9:93,9,0 chr1 287935 . A G 280.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.653;ClippingRankSum=2.26;DP=17;ExcessHet=3.0103;FS=15.315;MLEAC=1;MLEAF=0.500;MQ=37.35;MQRankSum=1.06;NEGATIVE_TRAIN_SITE;QD=16.52;ReadPosRankSum=0.955;SOR=4.977;VQSLOD=-3.632e+00;culprit=SOR GT:AD:DP:GQ:PL 0/1:6,11:17:99:309,0,144 chr1 288130 rs373366992 T C 71.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;ClippingRankSum=0.386;DB;DP=13;ExcessHet=3.0103;FS=5.119;MLEAC=1;MLEAF=0.500;MQ=39.15;MQRankSum=0.540;NEGATIVE_TRAIN_SITE;QD=5.52;ReadPosRankSum=0.540;SOR=0.039;VQSLOD=-1.783e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:9,4:13:99:100,0,271 chr1 290282 . T A 48.28 VQSRTrancheSNP99.95to100.00 AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.69;QD=16.09;SOR=2.833;VQSLOD=-4.444e+00;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,3:3:9:76,9,0 chr1 297604 rs756558238 TATA T 143 PASS AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.01;QD=27.64;SOR=1.609;VQSLOD=3.44;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:180,12,0 chr1 396651 . CAG C 187.87 PASS AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.70;QD=29.43;SOR=3.611;VQSLOD=4.47;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:225,15,0 chr1 408927 . G A 97.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.056e+00;ClippingRankSum=0.380;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.23;MQRankSum=0.718;QD=5.15;ReadPosRankSum=1.48;SOR=0.321;VQSLOD=-5.625e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:12,7:19:99:126,0,253 chr1 455371 . G A 64.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-5.500e-01;ClippingRankSum=-1.754e+00;DP=7;ExcessHet=3.0103;FS=15.441;MLEAC=1;MLEAF=0.500;MQ=22.37;MQRankSum=1.75;QD=9.25;ReadPosRankSum=-5.500e-01;SOR=3.221;VQSLOD=-4.307e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:3,4:7:53:93,0,53 chr1 492059 . G A 47.28 VQSRTrancheSNP99.95to100.00 AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.34;QD=15.76;SOR=2.833;VQSLOD=-4.360e+00;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,3:3:9:75,9,0 chr1 494515 rs576317820 T A 313.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.40;POSITIVE_TRAIN_SITE;QD=28.52;SOR=1.270;VQSLOD=3.54;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,11:11:33:342,33,0 chr1 503138 . GTATATA G 98.25 PASS AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=32.77;QD=32.75;SOR=2.833;VQSLOD=2.85;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 chr1 505074 . C T 523.77 PASS AC=2;AF=1.00;AN=2;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=21.92;QD=23.81;SOR=1.931;VQSLOD=-1.080e-02;culprit=QD GT:AD:DP:GQ:PL 1/1:0,22:22:65:552,65,0 chr1 505172 . T G 785.77 VQSRTrancheSNP99.95to100.00 AC=2;AF=1.00;AN=2;BaseQRankSum=-3.470e-01;ClippingRankSum=-2.480e-01;DP=35;ExcessHet=3.0103;FS=3.136;MLEAC=2;MLEAF=1.00;MQ=24.65;MQRankSum=-8.420e-01;QD=22.45;ReadPosRankSum=-1.733e+00;SOR=0.405;VQSLOD=-3.360e+00;culprit=QD GT:AD:DP:GQ:PL 1/1:1,34:35:80:814,80,0 chr1 505782 . C T 150.90 PASS AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.71;QD=30.18;SOR=3.611;VQSLOD=2.77;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,5:5:15:179,15,0 chr1 509574 . T C 57.28 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.24;QD=19.09;SOR=2.833;VQSLOD=-1.804e+00;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,3:3:9:85,9,0 chr1 511511 . C A 138.90 PASS AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=31.88;QD=27.78;SOR=3.611;VQSLOD=1.93;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,5:5:15:167,15,0 chr1 511562 rs62428730 C T 404.77 PASS AC=2;AF=1.00;AN=2;DB;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.85;QD=28.91;SOR=0.693;VQSLOD=3.73;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,14:14:42:433,42,0 chr1 514446 rs199492794 TA T 82.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.52;ClippingRankSum=1.19;DB;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.75;MQRankSum=-2.205e+00;QD=6.89;ReadPosRankSum=1.38;SOR=0.693;VQSLOD=2.39;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 0/1:6,6:12:99:1|0:514442_C_A:120,0,123 chr1 529806 . G A 421.77 PASS AC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=32.82;QD=30.09;SOR=0.693;VQSLOD=2.32;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,10:10:30:1|1:529806_G_A:450,30,0 chr1 529811 . C T 466.77 PASS AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=32.05;NEGATIVE_TRAIN_SITE;QD=31.26;SOR=0.859;VQSLOD=0.960;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,11:11:33:1|1:529806_G_A:495,33,0 chr1 529814 . C A 466.77 PASS AC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=32.05;QD=29.00;SOR=0.859;VQSLOD=2.76;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,11:11:33:1|1:529806_G_A:495,33,0 chr1 531472 . G C 130.84 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=21.89;QD=21.81;SOR=1.329;VQSLOD=-1.785e+00;culprit=QD GT:AD:DP:GQ:PL 1/1:0,6:6:18:159,18,0 chr1 531693 rs199491011 C T 138.84 PASS AC=2;AF=1.00;AN=2;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.67;QD=23.14;SOR=1.329;VQSLOD=0.074;culprit=QD GT:AD:DP:GQ:PL 1/1:0,6:6:18:167,18,0 chr1 586223 rs61767340 G A 83.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=2.13;ClippingRankSum=0.526;DB;DP=27;ExcessHet=3.0103;FS=1.983;MLEAC=1;MLEAF=0.500;MQ=32.11;MQRankSum=0.304;NEGATIVE_TRAIN_SITE;QD=3.10;ReadPosRankSum=-2.490e-01;SOR=1.609;VQSLOD=-2.632e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:20,7:27:99:112,0,454 chr1 588091 rs192687139 T C 59.28 VQSRTrancheSNP99.80to99.90 AC=2;AF=1.00;AN=2;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.26;QD=19.76;SOR=2.833;VQSLOD=-1.290e+00;culprit=QD GT:AD:DP:GQ:PL 1/1:0,3:3:9:87,9,0 chr1 588445 rs61767343 C T 222.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.56;ClippingRankSum=0.547;DB;DP=42;ExcessHet=3.0103;FS=4.805;MLEAC=1;MLEAF=0.500;MQ=27.40;MQRankSum=-4.140e-01;QD=5.30;ReadPosRankSum=1.96;SOR=1.549;VQSLOD=-3.725e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:28,14:42:99:251,0,619 chr1 588568 . C T 38.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.053;ClippingRankSum=0.896;DP=17;ExcessHet=3.0103;FS=15.315;MLEAC=1;MLEAF=0.500;MQ=23.75;MQRankSum=-2.055e+00;QD=2.28;ReadPosRankSum=-5.300e-02;SOR=3.592;VQSLOD=-4.261e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:12,5:17:67:67,0,290 chr1 591733 . C CAA 144.80 PASS AC=2;AF=1.00;AN=2;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.40;QD=24.13;SOR=2.303;VQSLOD=4.28;culprit=FS GT:AD:DP:GQ:PL 1/1:0,6:6:18:182,18,0 chr1 597920 rs374895564 G A 78.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.57;ClippingRankSum=-3.650e-01;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=38.80;MQRankSum=1.87;QD=7.88;ReadPosRankSum=-7.410e-01;SOR=0.412;VQSLOD=1.10;culprit=MQ GT:AD:DP:GQ:PL 0/1:6,4:10:99:107,0,114 chr1 598944 . G T 164.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.157e+00;ClippingRankSum=0.077;DP=13;ExcessHet=3.0103;FS=2.522;MLEAC=1;MLEAF=0.500;MQ=55.10;MQRankSum=-3.860e-01;NEGATIVE_TRAIN_SITE;QD=12.67;ReadPosRankSum=-3.860e-01;SOR=0.525;VQSLOD=-1.881e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:4,9:13:97:193,0,97 chr1 599948 . T TTGTG 162.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.590e-01;ClippingRankSum=-5.830e-01;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.39;MQRankSum=0.00;QD=13.56;ReadPosRankSum=-1.191e+00;SOR=0.307;VQSLOD=2.07;culprit=FS GT:AD:DP:GQ:PL 0/1:6,6:12:99:200,0,299 chr1 600428 rs373722660 A G 134.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.127;ClippingRankSum=-3.800e-01;DB;DP=19;ExcessHet=3.0103;FS=4.775;MLEAC=1;MLEAF=0.500;MQ=35.22;MQRankSum=-1.270e-01;NEGATIVE_TRAIN_SITE;QD=7.09;ReadPosRankSum=0.887;SOR=2.066;VQSLOD=-1.949e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:12,7:19:99:163,0,298 chr1 600822 rs149807327 T C 34.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.128;ClippingRankSum=0.128;DB;DP=22;ExcessHet=3.0103;FS=5.328;MLEAC=1;MLEAF=0.500;MQ=37.06;MQRankSum=-1.319e+00;NEGATIVE_TRAIN_SITE;QD=1.58;ReadPosRankSum=-2.596e+00;SOR=1.492;VQSLOD=-2.177e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:18,4:22:63:63,0,943 chr1 601667 . C T 55.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.567e+00;ClippingRankSum=2.30;DP=24;ExcessHet=3.0103;FS=1.935;MLEAC=1;MLEAF=0.500;MQ=28.06;MQRankSum=-1.900e+00;QD=2.32;ReadPosRankSum=-7.670e-01;SOR=1.238;VQSLOD=-2.758e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:18,6:24:84:84,0,440 chr1 602064 rs375649215 G A 104.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-5.480e-01;ClippingRankSum=-6.270e-01;DB;DP=22;ExcessHet=3.0103;FS=2.126;MLEAC=1;MLEAF=0.500;MQ=38.08;MQRankSum=0.313;NEGATIVE_TRAIN_SITE;QD=4.76;ReadPosRankSum=1.02;SOR=1.460;VQSLOD=-1.829e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:17,5:22:99:0|1:602064_G_A:133,0,715 chr1 602067 rs371573906 A G 107.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.571e+00;ClippingRankSum=1.66;DB;DP=20;ExcessHet=3.0103;FS=2.199;MLEAC=1;MLEAF=0.500;MQ=39.02;MQRankSum=0.175;NEGATIVE_TRAIN_SITE;QD=5.39;ReadPosRankSum=0.00;SOR=1.781;VQSLOD=-1.704e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:15,5:20:99:0|1:602064_G_A:136,0,686 chr1 602107 rs144672821 C T 113.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=0.887;ClippingRankSum=0.211;DB;DP=19;ExcessHet=3.0103;FS=1.984;MLEAC=1;MLEAF=0.500;MQ=46.22;MQRankSum=-2.240e+00;NEGATIVE_TRAIN_SITE;QD=5.99;ReadPosRankSum=0.887;SOR=1.609;VQSLOD=-9.466e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:12,7:19:99:142,0,322 chr1 602156 rs201044673 C G 170.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.887e+00;ClippingRankSum=-2.950e-01;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.05;MQRankSum=-3.005e+00;QD=11.38;ReadPosRankSum=0.295;SOR=0.646;VQSLOD=1.53;culprit=MQRankSum GT:AD:DP:GQ:PGT:PID:PL 0/1:9,6:15:99:0|1:602156_C_G:199,0,447 chr1 602157 rs201679166 A G 170.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.534e+00;ClippingRankSum=-5.300e-01;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.05;MQRankSum=-3.005e+00;QD=11.38;ReadPosRankSum=-5.300e-01;SOR=0.646;VQSLOD=1.65;culprit=MQRankSum GT:AD:DP:GQ:PGT:PID:PL 0/1:9,6:15:99:0|1:602156_C_G:199,0,447 chr1 605160 rs199511579 GC G 61.73 VQSRTrancheINDEL97.00to99.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.478e+00;ClippingRankSum=1.48;DB;DP=21;ExcessHet=3.0103;FS=10.985;MLEAC=1;MLEAF=0.500;MQ=33.52;MQRankSum=-1.120e+00;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=2.94;ReadPosRankSum=-3.130e-01;SOR=0.014;VQSLOD=0.483;culprit=QD GT:AD:DP:GQ:PL 0/1:17,4:21:99:99,0,610 chr1 609407 rs61769279 G C 42.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.757e+00;ClippingRankSum=-1.950e-01;DB;DP=34;ExcessHet=3.0103;FS=1.532;MLEAC=1;MLEAF=0.500;MQ=46.16;MQRankSum=0.117;NEGATIVE_TRAIN_SITE;QD=1.26;ReadPosRankSum=0.703;SOR=0.732;VQSLOD=-1.873e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:25,9:34:71:71,0,646 chr1 619415 . C G 109.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.491;ClippingRankSum=-2.020e-01;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=46.29;MQRankSum=-2.858e+00;QD=3.79;ReadPosRankSum=1.47;SOR=0.836;VQSLOD=1.61;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:24,5:29:99:0|1:619415_C_G:138,0,1314 chr1 619417 rs4120955 C T 109.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.30;ClippingRankSum=0.202;DB;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=46.29;MQRankSum=-2.858e+00;QD=3.79;ReadPosRankSum=0.895;SOR=0.836;VQSLOD=1.38;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:24,5:29:99:0|1:619415_C_G:138,0,1314 chr1 619428 rs78894760 G A 60.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.684;ClippingRankSum=0.091;DB;DP=32;ExcessHet=3.0103;FS=1.745;MLEAC=1;MLEAF=0.500;MQ=44.95;MQRankSum=-3.282e+00;NEGATIVE_TRAIN_SITE;QD=1.90;ReadPosRankSum=-4.100e-01;SOR=0.711;VQSLOD=-1.492e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:25,7:32:89:89,0,635 chr1 623863 . A G 60.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.905;ClippingRankSum=0.468;DP=27;ExcessHet=3.0103;FS=5.477;MLEAC=1;MLEAF=0.500;MQ=34.64;MQRankSum=1.72;NEGATIVE_TRAIN_SITE;QD=2.25;ReadPosRankSum=0.655;SOR=2.303;VQSLOD=-2.663e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:22,5:27:89:89,0,625 chr1 623988 . A G 208.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=3.06;ClippingRankSum=0.231;DP=26;ExcessHet=3.0103;FS=4.222;MLEAC=1;MLEAF=0.500;MQ=35.19;MQRankSum=-1.387e+00;NEGATIVE_TRAIN_SITE;QD=8.03;ReadPosRankSum=0.058;SOR=1.518;VQSLOD=-1.868e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:19,7:26:99:0|1:623988_A_G:237,0,992 chr1 623992 . C G 229.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=1.41;ClippingRankSum=-1.330e-01;DP=27;ExcessHet=3.0103;FS=3.771;MLEAC=1;MLEAF=0.500;MQ=35.64;MQRankSum=-1.248e+00;NEGATIVE_TRAIN_SITE;QD=8.51;ReadPosRankSum=-2.920e-01;SOR=1.034;VQSLOD=-1.825e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:19,8:27:99:0|1:623988_A_G:258,0,989 chr1 625776 rs150334593 T G 197.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.952;ClippingRankSum=-1.620e-01;DB;DP=28;ExcessHet=3.0103;FS=1.631;MLEAC=1;MLEAF=0.500;MQ=31.99;MQRankSum=-1.694e+00;NEGATIVE_TRAIN_SITE;QD=7.06;ReadPosRankSum=0.116;SOR=1.262;VQSLOD=-2.244e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:16,12:28:99:226,0,336 chr1 625960 . C A 58.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.545e+00;ClippingRankSum=0.271;DP=13;ExcessHet=3.0103;FS=11.228;MLEAC=1;MLEAF=0.500;MQ=23.89;MQRankSum=0.978;QD=4.52;ReadPosRankSum=0.437;SOR=3.596;VQSLOD=-3.929e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:8,5:13:87:87,0,189 chr1 627983 rs137905425 C T 222.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.630e+00;ClippingRankSum=0.360;DB;DP=30;ExcessHet=3.0103;FS=1.484;MLEAC=1;MLEAF=0.500;MQ=43.45;MQRankSum=-2.100e-02;NEGATIVE_TRAIN_SITE;QD=7.43;ReadPosRankSum=-8.260e-01;SOR=0.368;VQSLOD=-1.535e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:18,12:30:99:251,0,474 chr1 628245 rs78216996 T C 188.78 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=23.20;QD=23.60;SOR=4.407;VQSLOD=-2.055e+00;culprit=QD GT:AD:DP:GQ:PL 1/1:0,8:8:24:217,24,0 chr1 629906 rs1578391 C T 219.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=2.31;ClippingRankSum=0.340;DB;DP=73;ExcessHet=3.0103;FS=22.449;MLEAC=1;MLEAF=0.500;MQ=45.84;MQRankSum=-5.283e+00;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=3.23;ReadPosRankSum=1.47;SOR=2.684;VQSLOD=-7.300e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:51,17:68:99:248,0,1953 chr1 629915 rs538388406 A G 935.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.074e+00;ClippingRankSum=0.445;DB;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.29;MQRankSum=-6.173e+00;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=12.00;ReadPosRankSum=1.93;SOR=0.703;VQSLOD=-5.437e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:40,38:78:99:964,0,1030 chr1 630026 rs6594029 C T 75.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.576;ClippingRankSum=-9.700e-01;DB;DP=46;ExcessHet=3.0103;FS=24.624;MLEAC=1;MLEAF=0.500;MQ=52.51;MQRankSum=-4.129e+00;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=1.85;ReadPosRankSum=-1.990e+00;SOR=4.400;VQSLOD=-4.548e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:33,8:41:99:104,0,907 chr1 630039 rs55668158 C G 111.77 VQSRTrancheSNP99.50to99.60 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.450e-01;ClippingRankSum=0.902;DB;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.44;MQRankSum=1.86;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=2.54;ReadPosRankSum=1.11;SOR=0.713;VQSLOD=-7.417e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:35,9:44:99:140,0,924 chr1 630211 rs7416152 C T 272.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=1.93;ClippingRankSum=0.655;DB;DP=34;ExcessHet=3.0103;FS=1.533;MLEAC=1;MLEAF=0.500;MQ=51.94;MQRankSum=-4.285e+00;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=8.27;ReadPosRankSum=1.14;SOR=1.276;VQSLOD=-9.789e-01;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:21,12:33:99:301,0,535 chr1 630596 rs9283151 C T 216.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.180e+00;ClippingRankSum=0.208;DB;DP=26;ExcessHet=3.0103;FS=1.617;MLEAC=1;MLEAF=0.500;MQ=56.56;MQRankSum=-1.765e+00;NEGATIVE_TRAIN_SITE;QD=8.34;ReadPosRankSum=0.882;SOR=0.340;VQSLOD=-1.470e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:15,11:26:99:245,0,431 chr1 630668 rs6421780 G A 212.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;ClippingRankSum=-8.680e-01;DB;DP=22;ExcessHet=3.0103;FS=7.168;MLEAC=1;MLEAF=0.500;MQ=55.62;MQRankSum=-2.471e+00;NEGATIVE_TRAIN_SITE;QD=9.67;ReadPosRankSum=0.668;SOR=1.198;VQSLOD=-2.073e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:13,9:22:99:241,0,353 chr1 631859 rs78150957 CG C 457.73 PASS AC=2;AF=1.00;AN=2;DB;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.44;QD=32.70;SOR=2.303;VQSLOD=5.02;culprit=FS GT:AD:DP:GQ:PL 1/1:0,14:14:42:495,42,0 chr1 632834 rs373437560 C T 227.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.47;ClippingRankSum=0.983;DB;DP=28;ExcessHet=3.0103;FS=1.583;MLEAC=1;MLEAF=0.500;MQ=57.30;MQRankSum=1.18;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=8.13;ReadPosRankSum=1.51;SOR=0.967;VQSLOD=0.828;culprit=MQ GT:AD:DP:GQ:PL 0/1:18,10:28:99:256,0,438 chr1 633365 rs200850333 C CCA 117.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.719e+00;ClippingRankSum=0.196;DB;DP=31;ExcessHet=3.0103;FS=1.525;MLEAC=1;MLEAF=0.500;MQ=54.70;MQRankSum=-3.155e+00;NEGATIVE_TRAIN_SITE;QD=3.80;ReadPosRankSum=-8.490e-01;SOR=0.418;VQSLOD=-9.447e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:22,9:31:99:0|1:633365_C_CCA:155,0,853 chr1 633887 rs6650105 G A 703.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-7.000e-01;ClippingRankSum=0.037;DB;DP=52;ExcessHet=3.0103;FS=58.552;MLEAC=1;MLEAF=0.500;MQ=46.35;MQRankSum=-6.117e+00;POSITIVE_TRAIN_SITE;QD=13.53;ReadPosRankSum=-5.914e+00;SOR=5.350;VQSLOD=-2.118e+01;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:23,29:52:99:732,0,613 chr1 634112 rs6594033 T C 5228.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.174;ClippingRankSum=1.46;DB;DP=216;ExcessHet=3.0103;FS=104.324;MLEAC=1;MLEAF=0.500;MQ=33.35;MQRankSum=-7.403e+00;QD=25.02;ReadPosRankSum=0.192;SOR=5.959;VQSLOD=-1.237e+02;culprit=DP GT:AD:DP:GQ:PL 0/1:25,184:209:99:5257,0,178 chr1 634229 . A T 921.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-9.420e-01;ClippingRankSum=0.738;DP=58;ExcessHet=3.0103;FS=63.459;MLEAC=1;MLEAF=0.500;MQ=48.29;MQRankSum=-6.469e+00;QD=15.89;ReadPosRankSum=0.864;SOR=6.517;VQSLOD=-2.401e+01;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 0/1:33,25:58:99:0|1:634229_A_T:950,0,1458 chr1 634230 . C T 921.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.251;DP=58;ExcessHet=3.0103;FS=63.459;MLEAC=1;MLEAF=0.500;MQ=48.29;MQRankSum=-6.485e+00;QD=15.89;ReadPosRankSum=0.754;SOR=6.517;VQSLOD=-2.403e+01;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 0/1:33,25:58:99:0|1:634229_A_T:950,0,1458 chr1 634232 . A T 921.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.260e-01;ClippingRankSum=0.440;DP=58;ExcessHet=3.0103;FS=63.459;MLEAC=1;MLEAF=0.500;MQ=48.29;MQRankSum=-6.469e+00;QD=15.89;ReadPosRankSum=0.550;SOR=6.517;VQSLOD=-2.403e+01;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 0/1:33,25:58:99:0|1:634229_A_T:950,0,1458 chr1 634233 . G T 921.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.440;ClippingRankSum=-1.410e-01;DP=58;ExcessHet=3.0103;FS=63.459;MLEAC=1;MLEAF=0.500;MQ=48.29;MQRankSum=-6.469e+00;QD=15.89;ReadPosRankSum=0.314;SOR=6.517;VQSLOD=-2.404e+01;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 0/1:33,25:58:99:0|1:634229_A_T:950,0,1458 chr1 634234 . C T 921.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.115e+00;ClippingRankSum=-1.052e+00;DP=58;ExcessHet=3.0103;FS=63.459;MLEAC=1;MLEAF=0.500;MQ=48.29;MQRankSum=-6.469e+00;QD=15.89;ReadPosRankSum=0.141;SOR=6.517;VQSLOD=-2.405e+01;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 0/1:33,25:58:99:0|1:634229_A_T:950,0,1458 chr1 634237 . T TG 915.73 VQSRTrancheINDEL99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=2.26;ClippingRankSum=-5.870e-01;DP=57;ExcessHet=3.0103;FS=67.183;MLEAC=1;MLEAF=0.500;MQ=48.06;MQRankSum=-6.441e+00;QD=16.07;ReadPosRankSum=-7.480e-01;SOR=6.517;VQSLOD=-1.988e+01;culprit=MQRankSum GT:AD:DP:GQ:PGT:PID:PL 0/1:32,25:57:99:0|1:634229_A_T:953,0,1416 chr1 634239 . T TACGG 915.73 VQSRTrancheINDEL99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.07;ClippingRankSum=0.396;DP=56;ExcessHet=3.0103;FS=69.399;MLEAC=1;MLEAF=0.500;MQ=47.82;MQRankSum=-6.378e+00;QD=16.35;ReadPosRankSum=-1.352e+00;SOR=6.517;VQSLOD=-2.063e+01;culprit=MQRankSum GT:AD:DP:GQ:PGT:PID:PL 0/1:31,25:56:99:0|1:634229_A_T:953,0,1416 chr1 634241 rs796410684 A G 927.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.358e+00;ClippingRankSum=0.871;DB;DP=55;ExcessHet=3.0103;FS=66.078;MLEAC=1;MLEAF=0.500;MQ=47.57;MQRankSum=-6.347e+00;QD=16.87;ReadPosRankSum=-2.054e+00;SOR=6.517;VQSLOD=-2.582e+01;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 0/1:30,25:55:99:0|1:634229_A_T:956,0,1374 chr1 634244 rs6594035 T C 924.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.722e+00;ClippingRankSum=-1.154e+00;DB;DP=52;ExcessHet=3.0103;FS=69.169;MLEAC=1;MLEAF=0.500;MQ=46.75;MQRankSum=-6.172e+00;QD=17.78;ReadPosRankSum=-3.150e+00;SOR=6.517;VQSLOD=-2.800e+01;culprit=MQRankSum GT:AD:DP:GQ:PGT:PID:PL 0/1:27,25:52:99:0|1:634229_A_T:953,0,1416 chr1 634245 . ATTAACCTTC A 915.73 VQSRTrancheINDEL99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.926e+00;ClippingRankSum=0.382;DP=54;ExcessHet=3.0103;FS=61.640;MLEAC=1;MLEAF=0.500;MQ=46.78;MQRankSum=-6.297e+00;QD=16.96;ReadPosRankSum=-2.810e+00;SOR=6.517;VQSLOD=-1.822e+01;culprit=MQRankSum GT:AD:DP:GQ:PGT:PID:PL 0/1:29,25:54:99:0|1:634229_A_T:953,0,1404 chr1 634256 . C CGAGA 927.73 VQSRTrancheINDEL99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.198e+00;ClippingRankSum=0.668;DP=53;ExcessHet=3.0103;FS=66.767;MLEAC=1;MLEAF=0.500;MQ=46.21;MQRankSum=-6.245e+00;QD=17.50;ReadPosRankSum=-3.964e+00;SOR=6.517;VQSLOD=-2.063e+01;culprit=MQRankSum GT:AD:DP:GQ:PGT:PID:PL 0/1:28,25:53:99:0|1:634229_A_T:965,0,1236 chr1 634332 rs374132538 G A 277.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.73;ClippingRankSum=0.868;DB;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.66;MQRankSum=-7.830e-01;QD=9.26;ReadPosRankSum=0.953;SOR=0.693;VQSLOD=0.796;culprit=MQ GT:AD:DP:GQ:PL 0/1:18,12:30:99:306,0,453 chr1 634553 rs368347679 G A 272.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.16;ClippingRankSum=-6.690e-01;DB;DP=31;ExcessHet=3.0103;FS=5.961;MLEAC=1;MLEAF=0.500;MQ=55.21;MQRankSum=-1.683e+00;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=8.80;ReadPosRankSum=-3.040e-01;SOR=0.160;VQSLOD=-5.454e-01;culprit=MQ GT:AD:DP:GQ:PL 0/1:19,12:31:99:301,0,507 chr1 636513 . C A 45.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;ClippingRankSum=0.248;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=35.17;MQRankSum=2.05;QD=5.09;ReadPosRankSum=-2.480e-01;SOR=1.022;VQSLOD=0.851;culprit=QD GT:AD:DP:GQ:PL 0/1:6,3:9:74:74,0,163 chr1 642930 . G C 64.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.098e+00;ClippingRankSum=-6.760e-01;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.84;MQRankSum=0.470;QD=6.48;ReadPosRankSum=0.336;SOR=0.693;VQSLOD=-1.516e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:5,5:10:93:93,0,113 chr1 649307 . C T 144.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=1.31;ClippingRankSum=-3.790e-01;DP=25;ExcessHet=3.0103;FS=1.927;MLEAC=1;MLEAF=0.500;MQ=29.64;MQRankSum=1.02;QD=5.79;ReadPosRankSum=0.845;SOR=1.112;VQSLOD=-2.734e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:17,8:25:99:0|1:649307_C_T:173,0,458 chr1 649427 . C T 112.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.70;ClippingRankSum=-6.940e-01;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.93;MQRankSum=-1.157e+00;QD=8.67;ReadPosRankSum=1.31;SOR=0.223;VQSLOD=-3.487e-01;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:9,4:13:99:0|1:649427_C_T:141,0,407 chr1 649433 . C T 112.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.70;ClippingRankSum=-6.940e-01;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.93;MQRankSum=0.694;QD=8.67;ReadPosRankSum=0.386;SOR=0.223;VQSLOD=-4.818e-01;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:9,4:13:99:0|1:649427_C_T:141,0,407 chr1 653702 . GAGAA G 53.70 PASS AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.89;QD=26.85;SOR=2.303;VQSLOD=4.32;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 chr1 656888 rs369475281 G T 354.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-8.140e-01;ClippingRankSum=-2.140e-01;DB;DP=39;ExcessHet=3.0103;FS=2.869;MLEAC=1;MLEAF=0.500;MQ=48.53;MQRankSum=-2.727e+00;NEGATIVE_TRAIN_SITE;QD=9.10;ReadPosRankSum=-7.280e-01;SOR=1.244;VQSLOD=-1.634e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:23,16:39:99:383,0,644 chr1 665761 rs140845213 C T 102.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.460e-01;ClippingRankSum=-4.370e-01;DB;DP=26;ExcessHet=3.0103;FS=1.800;MLEAC=1;MLEAF=0.500;MQ=35.43;MQRankSum=-2.418e+00;NEGATIVE_TRAIN_SITE;QD=4.11;ReadPosRankSum=-5.530e-01;SOR=1.356;VQSLOD=-1.914e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:17,8:25:99:131,0,394 chr1 666028 rs143332664 G A 30.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=1.87;ClippingRankSum=-9.620e-01;DB;DP=17;ExcessHet=3.0103;FS=6.021;MLEAC=1;MLEAF=0.500;MQ=32.18;MQRankSum=-2.095e+00;NEGATIVE_TRAIN_SITE;QD=1.81;ReadPosRankSum=1.08;SOR=1.447;VQSLOD=-2.261e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:13,4:17:59:59,0,253 chr1 666461 rs148361140 G C 51.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.18;ClippingRankSum=-8.030e-01;DB;DP=20;ExcessHet=3.0103;FS=15.849;MLEAC=1;MLEAF=0.500;MQ=30.72;MQRankSum=1.28;QD=2.59;ReadPosRankSum=0.331;SOR=3.229;VQSLOD=-3.369e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:16,4:20:80:80,0,405 chr1 667265 rs200919600 C T 31.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.891;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.06;MQRankSum=-2.517e+00;QD=1.32;ReadPosRankSum=-5.810e-01;SOR=0.627;VQSLOD=1.30;culprit=QD GT:AD:DP:GQ:PL 0/1:20,4:24:60:60,0,534 chr1 690714 . T A 43.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.84;ClippingRankSum=0.289;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=26.50;MQRankSum=-6.000e-01;QD=3.65;ReadPosRankSum=0.536;SOR=0.941;VQSLOD=0.712;culprit=QD GT:AD:DP:GQ:PL 0/1:8,4:12:72:72,0,148 chr1 691396 rs770009340 G GC 258.73 VQSRTrancheINDEL99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.148;ClippingRankSum=1.13;DB;DP=49;ExcessHet=3.0103;FS=11.560;MLEAC=1;MLEAF=0.500;MQ=30.55;MQRankSum=3.05;NEGATIVE_TRAIN_SITE;QD=5.50;ReadPosRankSum=-2.170e-01;SOR=1.854;VQSLOD=-4.704e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:32,15:47:99:296,0,802 chr1 693086 . A C 91.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.120e-01;ClippingRankSum=-7.410e-01;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.94;MQRankSum=-1.905e+00;QD=5.74;ReadPosRankSum=-8.470e-01;SOR=0.473;VQSLOD=0.435;culprit=QD GT:AD:DP:GQ:PL 0/1:9,7:16:99:120,0,190 chr1 700590 rs200380870 A C 87.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=21.67;QD=29.09;SOR=1.179;VQSLOD=0.781;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,3:3:9:1|1:700590_A_C:115,9,0 chr1 700596 . C T 62.74 PASS AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=21.51;QD=31.37;SOR=0.693;VQSLOD=0.749;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:700590_A_C:90,6,0 chr1 700602 . C T 62.74 PASS AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=21.51;QD=31.37;SOR=0.693;VQSLOD=0.813;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:700590_A_C:90,6,0 chr1 700641 rs3857304 G A 98.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=21.01;QD=19.78;SOR=1.022;VQSLOD=-6.389e-01;culprit=QD GT:AD:DP:GQ:PL 1/1:0,5:5:15:127,15,0 chr1 700664 rs4030160 G A 133.84 PASS AC=2;AF=1.00;AN=2;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.05;QD=22.31;SOR=1.329;VQSLOD=-4.481e-01;culprit=QD GT:AD:DP:GQ:PL 1/1:0,6:6:18:162,18,0 chr1 700736 rs61769323 G C 172.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.85;QD=21.60;SOR=1.863;VQSLOD=0.048;culprit=QD GT:AD:DP:GQ:PL 1/1:0,8:8:24:201,24,0 chr1 714717 rs200021096 A G 246.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.69;QD=22.43;SOR=1.270;VQSLOD=-7.070e-02;culprit=QD GT:AD:DP:GQ:PL 1/1:0,11:11:32:275,32,0 chr1 715697 rs760939004 T C 58.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.54;ClippingRankSum=-4.060e-01;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.63;MQRankSum=0.406;QD=9.79;ReadPosRankSum=1.54;SOR=0.693;VQSLOD=1.32;culprit=DP GT:AD:DP:GQ:PL 0/1:3,3:6:87:87,0,104 chr1 715769 rs199959440 C T 213.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.11;ClippingRankSum=-2.069e+00;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=42.34;MQRankSum=-1.010e+00;QD=12.57;ReadPosRankSum=1.11;SOR=0.859;VQSLOD=1.99;culprit=MQ GT:AD:DP:GQ:PL 0/1:8,9:17:99:242,0,167 chr1 715972 rs377611181 C T 39.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;ClippingRankSum=-1.203e+00;DB;DP=9;ExcessHet=3.0103;FS=7.782;MLEAC=1;MLEAF=0.500;MQ=27.03;MQRankSum=0.573;QD=4.42;ReadPosRankSum=0.573;SOR=2.795;VQSLOD=-3.185e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:6,3:9:68:68,0,147 chr1 722408 rs760310201 G C 337.77 PASS AC=2;AF=1.00;AN=2;DB;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.94;QD=24.13;SOR=1.765;VQSLOD=1.15;culprit=QD GT:AD:DP:GQ:PL 1/1:0,14:14:42:366,42,0 chr1 725086 . C G 112.90 PASS AC=2;AF=1.00;AN=2;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=27.40;QD=22.58;SOR=1.981;VQSLOD=0.268;culprit=QD GT:AD:DP:GQ:PL 1/1:0,5:5:15:141,15,0 chr1 726821 rs202070913 G A 96.90 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DB;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.20;QD=19.38;SOR=3.611;VQSLOD=-2.170e+00;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,5:5:15:125,15,0 chr1 727477 rs377354243 G A 272.77 PASS AC=2;AF=1.00;AN=2;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.32;QD=27.28;SOR=0.693;VQSLOD=1.52;culprit=QD GT:AD:DP:GQ:PL 1/1:0,10:10:30:301,30,0 chr1 727717 rs61769340 G C 598.77 PASS AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=24.96;QD=24.95;SOR=0.859;VQSLOD=0.898;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,24:24:71:1|1:727717_G_C:627,71,0 chr1 732286 rs201764515 T A 72.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=35.71;QD=24.09;SOR=2.833;VQSLOD=1.27;culprit=QD GT:AD:DP:GQ:PL 1/1:0,3:3:9:100,9,0 chr1 736717 . A G 85.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.319e+00;ClippingRankSum=1.66;DP=22;ExcessHet=3.0103;FS=5.959;MLEAC=1;MLEAF=0.500;MQ=45.84;MQRankSum=-8.090e-01;NEGATIVE_TRAIN_SITE;QD=3.90;ReadPosRankSum=-1.405e+00;SOR=2.876;VQSLOD=-1.348e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:18,4:22:99:0|1:736717_A_G:114,0,744 chr1 736723 . A AT 76.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.234e+00;ClippingRankSum=0.638;DP=22;ExcessHet=3.0103;FS=5.959;MLEAC=1;MLEAF=0.500;MQ=45.84;MQRankSum=-8.090e-01;QD=3.49;ReadPosRankSum=-1.234e+00;SOR=2.876;VQSLOD=-1.286e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:18,4:22:99:0|1:736717_A_G:114,0,744 chr1 736724 . A C 85.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.745e+00;ClippingRankSum=0.638;DP=22;ExcessHet=3.0103;FS=5.959;MLEAC=1;MLEAF=0.500;MQ=45.84;MQRankSum=-8.090e-01;NEGATIVE_TRAIN_SITE;QD=3.90;ReadPosRankSum=-1.234e+00;SOR=2.876;VQSLOD=-1.328e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:18,4:22:99:114,0,744 chr1 736727 . A G 82.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.879e+00;ClippingRankSum=0.122;DP=23;ExcessHet=3.0103;FS=5.902;MLEAC=1;MLEAF=0.500;MQ=45.94;MQRankSum=-7.710e-01;NEGATIVE_TRAIN_SITE;QD=3.60;ReadPosRankSum=-7.710e-01;SOR=2.712;VQSLOD=-1.261e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:19,4:23:99:0|1:736717_A_G:111,0,786 chr1 736731 . G GTC 70.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.014e+00;ClippingRankSum=-3.650e-01;DP=23;ExcessHet=3.0103;FS=5.902;MLEAC=1;MLEAF=0.500;MQ=45.94;MQRankSum=-7.710e-01;QD=3.08;ReadPosRankSum=-6.890e-01;SOR=2.712;VQSLOD=-5.831e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:19,4:23:99:0|1:736717_A_G:108,0,828 chr1 736732 . G GC 70.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.123e+00;ClippingRankSum=-5.270e-01;DP=23;ExcessHet=3.0103;FS=5.902;MLEAC=1;MLEAF=0.500;MQ=45.94;MQRankSum=-7.710e-01;QD=3.08;ReadPosRankSum=-4.460e-01;SOR=2.712;VQSLOD=-5.552e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:19,4:23:99:0|1:736717_A_G:108,0,828 chr1 736735 . T TATC 67.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.068e+00;ClippingRankSum=-5.270e-01;DP=23;ExcessHet=3.0103;FS=5.902;MLEAC=1;MLEAF=0.500;MQ=46.23;MQRankSum=-7.710e-01;QD=2.94;ReadPosRankSum=-1.220e-01;SOR=2.712;VQSLOD=-5.775e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:19,4:23:99:0|1:736717_A_G:105,0,870 chr1 736736 . G A 79.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.053e+00;ClippingRankSum=-1.160e-01;DP=24;ExcessHet=3.0103;FS=5.814;MLEAC=1;MLEAF=0.500;MQ=46.26;MQRankSum=-7.360e-01;NEGATIVE_TRAIN_SITE;QD=3.32;ReadPosRankSum=0.039;SOR=2.564;VQSLOD=-1.202e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:20,4:24:99:0|1:736717_A_G:108,0,828 chr1 736740 . AGCTTGTTTTCC A 61.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-9.210e-01;ClippingRankSum=0.375;DP=27;ExcessHet=3.0103;FS=5.724;MLEAC=1;MLEAF=0.500;MQ=45.97;MQRankSum=-7.850e-01;NEGATIVE_TRAIN_SITE;QD=2.29;ReadPosRankSum=0.408;SOR=2.494;VQSLOD=-8.703e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:23,4:27:99:0|1:736717_A_G:99,0,954 chr1 736751 . C CAAAA 61.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.399e+00;ClippingRankSum=0.375;DP=27;ExcessHet=3.0103;FS=5.724;MLEAC=1;MLEAF=0.500;MQ=45.97;MQRankSum=-7.850e-01;NEGATIVE_TRAIN_SITE;QD=2.29;ReadPosRankSum=0.648;SOR=2.494;VQSLOD=-8.965e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:23,4:27:99:0|1:736717_A_G:99,0,954 chr1 736829 rs79279787 G A 196.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=1.24;ClippingRankSum=-4.200e-02;DB;DP=42;ExcessHet=3.0103;FS=1.307;MLEAC=1;MLEAF=0.500;MQ=42.29;MQRankSum=-1.350e+00;NEGATIVE_TRAIN_SITE;QD=4.68;ReadPosRankSum=0.905;SOR=0.923;VQSLOD=-2.285e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:30,12:42:99:225,0,686 chr1 736950 rs530588710 G C 146.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.68;ClippingRankSum=1.35;DB;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.47;MQRankSum=1.14;POSITIVE_TRAIN_SITE;QD=5.44;ReadPosRankSum=0.664;SOR=0.859;VQSLOD=1.32;culprit=QD GT:AD:DP:GQ:PL 0/1:19,8:27:99:175,0,431 chr1 737283 rs371072735 T G 88.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.106e+00;ClippingRankSum=-2.000e-02;DB;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.34;MQRankSum=-1.238e+00;NEGATIVE_TRAIN_SITE;QD=2.61;ReadPosRankSum=1.12;SOR=0.527;VQSLOD=-7.894e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:26,8:34:99:117,0,720 chr1 737443 rs4951925 C G 321.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=2.58;ClippingRankSum=0.445;DB;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.11;MQRankSum=-4.649e+00;NEGATIVE_TRAIN_SITE;QD=6.70;ReadPosRankSum=-1.560e-01;SOR=0.756;VQSLOD=-2.162e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:33,15:48:99:350,0,900 chr1 737737 rs200073030 T C 414.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.559e+00;ClippingRankSum=0.155;DB;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.17;MQRankSum=-4.931e+00;NEGATIVE_TRAIN_SITE;QD=10.64;ReadPosRankSum=0.716;SOR=0.941;VQSLOD=-9.642e-01;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:20,19:39:99:443,0,561 chr1 737843 rs201987734 T G 95.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.020;ClippingRankSum=-1.120e+00;DB;DP=35;ExcessHet=3.0103;FS=1.675;MLEAC=1;MLEAF=0.500;MQ=37.64;MQRankSum=-2.180e+00;NEGATIVE_TRAIN_SITE;QD=2.74;ReadPosRankSum=-3.730e-01;SOR=1.312;VQSLOD=-2.220e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:27,8:35:99:124,0,711 chr1 737856 rs9768594 G T 102.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=1.20;ClippingRankSum=0.648;DB;DP=35;ExcessHet=3.0103;FS=1.675;MLEAC=1;MLEAF=0.500;MQ=38.08;MQRankSum=-2.062e+00;NEGATIVE_TRAIN_SITE;QD=2.94;ReadPosRankSum=-3.730e-01;SOR=1.312;VQSLOD=-2.182e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:27,8:35:99:131,0,686 chr1 737947 rs71221966 G A 96.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.531;ClippingRankSum=-1.114e+00;DB;DP=28;ExcessHet=3.0103;FS=12.067;MLEAC=1;MLEAF=0.500;MQ=38.89;MQRankSum=-1.273e+00;NEGATIVE_TRAIN_SITE;QD=3.46;ReadPosRankSum=2.60;SOR=3.660;VQSLOD=-2.595e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:21,7:28:99:125,0,561 chr1 738516 . T C 62.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.670e-01;ClippingRankSum=0.100;DP=24;ExcessHet=3.0103;FS=8.098;MLEAC=1;MLEAF=0.500;MQ=29.57;MQRankSum=-1.167e+00;QD=2.62;ReadPosRankSum=-1.700e+00;SOR=2.245;VQSLOD=-2.962e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:18,6:24:91:91,0,473 chr1 738729 . A G 33.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.362e+00;ClippingRankSum=-2.360e-01;DP=42;ExcessHet=3.0103;FS=3.837;MLEAC=1;MLEAF=0.500;MQ=33.59;MQRankSum=-2.160e+00;NEGATIVE_TRAIN_SITE;QD=0.80;ReadPosRankSum=-4.390e-01;SOR=0.659;VQSLOD=-3.362e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:35,7:42:62:62,0,952 chr1 738756 . T C 46.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-6.700e-02;ClippingRankSum=1.55;DP=48;ExcessHet=3.0103;FS=1.957;MLEAC=1;MLEAF=0.500;MQ=33.46;MQRankSum=-1.721e+00;NEGATIVE_TRAIN_SITE;QD=0.97;ReadPosRankSum=-1.789e+00;SOR=1.329;VQSLOD=-3.991e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:43,5:48:75:0|1:738756_T_C:75,0,2071 chr1 738766 . G A 55.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=2.98;ClippingRankSum=-1.800e-02;DP=45;ExcessHet=3.0103;FS=1.931;MLEAC=1;MLEAF=0.500;MQ=33.53;MQRankSum=-1.643e+00;NEGATIVE_TRAIN_SITE;QD=1.24;ReadPosRankSum=-1.968e+00;SOR=1.214;VQSLOD=-3.721e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:40,5:45:84:0|1:738756_T_C:84,0,2001 chr1 739041 rs200806899 A T 880.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.945e+00;ClippingRankSum=0.780;DB;DP=40;ExcessHet=3.0103;FS=1.452;MLEAC=1;MLEAF=0.500;MQ=43.23;MQRankSum=-4.678e+00;NEGATIVE_TRAIN_SITE;QD=22.02;ReadPosRankSum=1.44;SOR=0.390;VQSLOD=-2.048e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:13,27:40:99:909,0,343 chr1 739054 rs74564050 A T 363.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.081e+00;ClippingRankSum=-8.700e-02;DB;DP=44;ExcessHet=3.0103;FS=2.774;MLEAC=1;MLEAF=0.500;MQ=44.47;MQRankSum=-2.223e+00;NEGATIVE_TRAIN_SITE;QD=8.46;ReadPosRankSum=-1.860e-01;SOR=0.354;VQSLOD=-2.089e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:26,17:43:99:392,0,1271 chr1 739076 rs368813658 G A 189.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=2.11;ClippingRankSum=0.732;DB;DP=44;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=44.65;MQRankSum=-3.280e+00;NEGATIVE_TRAIN_SITE;QD=4.31;ReadPosRankSum=0.352;SOR=0.892;VQSLOD=-1.710e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:33,11:44:99:218,0,1132 chr1 739602 rs773974007 A AT 193.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.675;ClippingRankSum=2.34;DB;DP=29;ExcessHet=3.0103;FS=2.120;MLEAC=1;MLEAF=0.500;MQ=24.93;MQRankSum=-1.816e+00;NEGATIVE_TRAIN_SITE;QD=7.45;ReadPosRankSum=0.00;SOR=1.352;VQSLOD=-1.582e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:15,11:26:99:231,0,335 chr1 740738 rs146067153 C T 307.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.643;ClippingRankSum=1.52;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=39.53;MQRankSum=-3.860e-01;POSITIVE_TRAIN_SITE;QD=11.84;ReadPosRankSum=-4.890e-01;SOR=0.619;VQSLOD=2.75;culprit=MQ GT:AD:DP:GQ:PL 0/1:12,14:26:99:336,0,258 chr1 744224 rs139961686 C A 438.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.62;QD=27.42;SOR=3.258;VQSLOD=1.83;culprit=QD GT:AD:DP:GQ:PL 1/1:0,16:16:48:467,48,0 chr1 744312 rs377059754 C T 79.03 VQSRTrancheSNP99.80to99.90 AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.00;QD=19.76;SOR=3.258;VQSLOD=-1.532e+00;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,4:4:12:107,12,0 chr1 749482 rs61769348 G A 64.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.330e-01;ClippingRankSum=0.696;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.63;MQRankSum=0.271;NEGATIVE_TRAIN_SITE;QD=4.98;ReadPosRankSum=-1.256e+00;SOR=1.179;VQSLOD=-1.035e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:8,5:13:93:93,0,211 chr1 754591 rs200318145 T C 42.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.447e+00;ClippingRankSum=0.00;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.31;MQRankSum=0.00;QD=4.28;ReadPosRankSum=0.741;SOR=0.412;VQSLOD=-6.377e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:6,4:10:71:71,0,119 chr1 754949 rs200877292 C T 50.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.75;ClippingRankSum=0.095;DB;DP=25;ExcessHet=3.0103;FS=4.222;MLEAC=1;MLEAF=0.500;MQ=21.63;MQRankSum=-2.450e+00;QD=2.03;ReadPosRankSum=1.37;SOR=1.206;VQSLOD=-3.601e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:19,6:25:79:79,0,406 chr1 766566 rs61769353 A G 587.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.29;QD=29.39;SOR=0.693;VQSLOD=2.34;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,20:20:60:616,60,0 chr1 768987 rs9727436 T C 167.78 VQSRTrancheSNP99.60to99.80 AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=31.42;NEGATIVE_TRAIN_SITE;QD=20.97;SOR=2.833;VQSLOD=-9.377e-01;culprit=QD GT:AD:DP:GQ:PL 1/1:0,8:8:24:196,24,0 chr1 769719 . G A 54.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.135;ClippingRankSum=-3.800e-01;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.78;MQRankSum=-1.309e+00;QD=4.56;ReadPosRankSum=-3.800e-01;SOR=0.760;VQSLOD=1.56;culprit=QD GT:AD:DP:GQ:PL 0/1:7,5:12:83:83,0,157 chr1 770502 rs72631875 G A 238.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.65;ClippingRankSum=-2.080e-01;DB;DP=26;ExcessHet=3.0103;FS=3.682;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=0.156;POSITIVE_TRAIN_SITE;QD=9.18;ReadPosRankSum=1.40;SOR=1.115;VQSLOD=1.47;culprit=QD GT:AD:DP:GQ:PL 0/1:15,11:26:99:267,0,327 chr1 770988 rs12029736 A G 554.77 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.58;ClippingRankSum=-6.780e-01;DB;DP=23;ExcessHet=3.0103;FS=3.203;MLEAC=2;MLEAF=1.00;MQ=48.21;MQRankSum=-1.131e+00;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=24.12;ReadPosRankSum=-1.583e+00;SOR=0.499;VQSLOD=0.158;culprit=QD GT:AD:DP:GQ:PL 1/1:1,22:23:58:583,58,0 chr1 771398 rs113462541 G A 331.77 PASS AC=2;AF=1.00;AN=2;DB;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.18;POSITIVE_TRAIN_SITE;QD=23.70;SOR=0.976;VQSLOD=2.04;culprit=QD GT:AD:DP:GQ:PL 1/1:0,14:14:41:360,41,0 chr1 772711 rs372626744 A G 128.84 VQSRTrancheSNP99.80to99.90 AC=2;AF=1.00;AN=2;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=24.49;QD=21.47;SOR=3.912;VQSLOD=-1.192e+00;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,6:6:18:157,18,0 chr1 775840 . C CA 53.90 PASS AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.94;QD=10.78;SOR=3.611;VQSLOD=1.81;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:14:91,14,0 chr1 779047 rs12028261 G A 808.77 PASS AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=46.29;POSITIVE_TRAIN_SITE;QD=32.35;SOR=0.770;VQSLOD=5.04;culprit=QD GT:AD:DP:GQ:PL 1/1:0,25:25:75:837,75,0 chr1 779968 rs3131984 T G 739.77 PASS AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=30.82;SOR=1.270;VQSLOD=22.54;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,24:24:72:768,72,0 chr1 780616 rs4614203 A T 171.80 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=42.35;QD=24.54;SOR=1.609;VQSLOD=2.54;culprit=QD GT:AD:DP:GQ:PL 1/1:0,7:7:21:200,21,0 chr1 783006 rs10900602 A G 323.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.39;POSITIVE_TRAIN_SITE;QD=29.43;SOR=2.494;VQSLOD=4.05;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,11:11:33:352,33,0 chr1 783175 rs10751453 T C 712.77 PASS AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.18;QD=28.51;SOR=1.893;VQSLOD=4.51;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,25:25:74:741,74,0 chr1 784860 rs3121393 T C 686.77 PASS AC=2;AF=1.00;AN=2;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.60;POSITIVE_TRAIN_SITE;QD=31.22;SOR=0.874;VQSLOD=4.87;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,22:22:66:715,66,0 chr1 785417 rs3115846 G A 624.77 PASS AC=2;AF=1.00;AN=2;DB;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.93;POSITIVE_TRAIN_SITE;QD=32.88;SOR=1.292;VQSLOD=5.20;culprit=QD GT:AD:DP:GQ:PL 1/1:0,19:19:57:653,57,0 chr1 788418 rs34882115 CAG C 286.75 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.94;POSITIVE_TRAIN_SITE;QD=26.28;SOR=1.179;VQSLOD=6.91;culprit=FS GT:AD:DP:GQ:PL 1/1:0,8:8:24:324,24,0 chr1 788511 rs2977670 G C 433.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.08;POSITIVE_TRAIN_SITE;QD=28.92;SOR=1.112;VQSLOD=4.59;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,15:15:45:462,45,0 chr1 788757 rs374587598 T TAATGG 160.90 PASS AC=2;AF=1.00;AN=2;DB;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.42;QD=30.19;SOR=0.693;VQSLOD=3.54;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:14:198,14,0 chr1 789489 rs12735556 C A 295.84 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.751;ClippingRankSum=0.751;DB;DP=14;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=49.39;MQRankSum=-7.510e-01;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=32.87;ReadPosRankSum=0.751;SOR=1.739;VQSLOD=-1.121e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:1,8:9:18:0|1:789489_C_A:324,0,18 chr1 789491 rs12735557 C G 295.84 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.747;ClippingRankSum=-7.470e-01;DB;DP=13;ExcessHet=3.0103;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=48.48;MQRankSum=0.747;NEGATIVE_TRAIN_SITE;QD=29.45;ReadPosRankSum=0.747;SOR=1.447;VQSLOD=-1.962e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:1,7:8:18:0|1:789489_C_A:324,0,18 chr1 789502 rs62653102 T C 217.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.720e-01;ClippingRankSum=0.572;DB;DP=13;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=48.48;MQRankSum=-5.720e-01;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=27.22;ReadPosRankSum=0.572;SOR=1.061;VQSLOD=-1.015e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:2,6:8:66:0|1:789489_C_A:246,0,66 chr1 789503 rs200283906 G A 217.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-5.720e-01;DB;DP=13;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=48.48;MQRankSum=0.00;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=27.22;ReadPosRankSum=0.572;SOR=1.061;VQSLOD=-1.066e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:2,6:8:66:0|1:789489_C_A:246,0,66 chr1 789504 rs201300314 G C 214.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-5.720e-01;ClippingRankSum=-5.720e-01;DB;DP=13;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=48.48;MQRankSum=-1.067e+00;NEGATIVE_TRAIN_SITE;QD=26.85;ReadPosRankSum=0.00;SOR=1.061;VQSLOD=-1.469e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:2,6:8:99:0|1:789489_C_A:243,0,108 chr1 789506 rs199596027 G C 214.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.054e+00;ClippingRankSum=1.00;DB;DP=14;ExcessHet=3.0103;FS=2.808;MLEAC=1;MLEAF=0.500;MQ=49.39;MQRankSum=-1.001e+00;NEGATIVE_TRAIN_SITE;QD=23.86;ReadPosRankSum=0.248;SOR=1.170;VQSLOD=-1.309e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:3,6:9:99:0|1:789489_C_A:243,0,108 chr1 789508 rs111203391 G A 214.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.684;ClippingRankSum=0.322;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=48.48;MQRankSum=0.322;QD=26.85;ReadPosRankSum=0.550;SOR=0.799;VQSLOD=2.10;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:3,5:8:99:0|1:789489_C_A:243,0,108 chr1 789510 rs747843478 T C 172.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.221e+00;ClippingRankSum=0.322;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=48.48;MQRankSum=-1.517e+00;QD=21.60;ReadPosRankSum=0.550;SOR=0.799;VQSLOD=2.09;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:3,5:8:99:0|1:789489_C_A:201,0,111 chr1 789514 . TTCAAA T 160.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.31;ClippingRankSum=0.361;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.39;MQRankSum=-1.652e+00;QD=17.86;ReadPosRankSum=-9.370e-01;SOR=1.022;VQSLOD=2.61;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 0/1:4,5:9:99:0|1:789489_C_A:198,0,118 chr1 789568 rs200087344 TATGGA T 322.75 PASS AC=2;AF=1.00;AN=2;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.21;QD=34.04;SOR=1.179;VQSLOD=4.99;culprit=FS GT:AD:DP:GQ:PL 1/1:0,8:8:24:360,24,0 chr1 790933 rs200420414 CGAATGGAATG C 82.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.23;ClippingRankSum=-1.231e+00;DB;DP=7;ExcessHet=3.0103;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=48.89;MQRankSum=1.23;QD=16.55;ReadPosRankSum=0.358;SOR=2.833;VQSLOD=-6.171e-01;culprit=SOR GT:AD:DP:GQ:PL 0/1:2,3:5:75:120,0,75 chr1 791101 rs3131980 T G 478.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.46;QD=28.16;SOR=1.371;VQSLOD=4.83;culprit=QD GT:AD:DP:GQ:PL 1/1:0,17:17:51:507,51,0 chr1 791544 rs762353340 TGAATG T 80.25 PASS AC=2;AF=1.00;AN=2;DB;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=31.62;QD=26.75;SOR=1.179;VQSLOD=4.61;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:117,9,0 chr1 792149 rs566981575 A G 237.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.373e+00;ClippingRankSum=1.09;DB;DP=21;ExcessHet=3.0103;FS=1.971;MLEAC=1;MLEAF=0.500;MQ=39.48;MQRankSum=0.035;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=11.32;ReadPosRankSum=-2.460e-01;SOR=0.307;VQSLOD=7.800e-03;culprit=MQ GT:AD:DP:GQ:PL 0/1:11,10:21:99:266,0,323 chr1 792779 rs3131978 C T 425.77 PASS AC=2;AF=1.00;AN=2;DB;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=32.13;POSITIVE_TRAIN_SITE;QD=30.41;SOR=2.303;VQSLOD=3.86;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,14:14:42:454,42,0 chr1 792862 rs3131977 C G 294.77 PASS AC=2;AF=1.00;AN=2;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=46.47;POSITIVE_TRAIN_SITE;QD=29.48;SOR=2.303;VQSLOD=5.62;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,10:10:30:323,30,0 chr1 794299 rs4951859 C G 1093.77 PASS AC=2;AF=1.00;AN=2;DB;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.14;POSITIVE_TRAIN_SITE;QD=30.38;SOR=0.927;VQSLOD=5.34;culprit=DP GT:AD:DP:GQ:PL 1/1:0,36:36:99:1122,107,0 chr1 797392 rs541848210 G A 351.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.115e+00;ClippingRankSum=-1.660e-01;DB;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=48.89;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=11.73;ReadPosRankSum=-4.100e-02;SOR=0.721;VQSLOD=2.99;culprit=MQ GT:AD:DP:GQ:PL 0/1:15,15:30:99:380,0,429 chr1 798618 rs61770164 C T 70.03 VQSRTrancheSNP99.90to99.95 AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=30.34;QD=17.51;SOR=3.258;VQSLOD=-2.987e+00;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,4:4:12:98,12,0 chr1 798662 rs61770165 G A 39.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.12;NEGATIVE_TRAIN_SITE;QD=19.87;SOR=0.693;VQSLOD=0.547;culprit=QD GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0 chr1 799082 rs12564807 G A 233.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.76;QD=29.22;SOR=1.179;VQSLOD=3.89;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,8:8:24:262,24,0 chr1 799111 rs7518433 T C 274.78 PASS AC=2;AF=1.00;AN=2;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=46.49;POSITIVE_TRAIN_SITE;QD=30.53;SOR=0.892;VQSLOD=5.47;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,9:9:27:303,27,0 chr1 799559 rs761625058 C CT 239.73 VQSRTrancheINDEL99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.704e+00;ClippingRankSum=0.102;DB;DP=32;ExcessHet=3.0103;FS=3.467;MLEAC=1;MLEAF=0.500;MQ=49.38;MQRankSum=-3.923e+00;NEGATIVE_TRAIN_SITE;QD=7.49;ReadPosRankSum=0.142;SOR=0.904;VQSLOD=-2.299e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:22,10:32:99:277,0,728 chr1 799571 rs61770166 A G 138.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.175e+00;ClippingRankSum=-4.270e-01;DB;DP=32;ExcessHet=3.0103;FS=5.743;MLEAC=1;MLEAF=0.500;MQ=50.83;MQRankSum=-3.883e+00;NEGATIVE_TRAIN_SITE;QD=4.34;ReadPosRankSum=-4.680e-01;SOR=0.842;VQSLOD=-2.169e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:22,10:32:99:167,0,608 chr1 800046 rs199800910 G A 150.81 PASS AC=2;AF=1.00;AN=2;DB;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=31.27;NEGATIVE_TRAIN_SITE;QD=21.54;SOR=0.941;VQSLOD=0.726;culprit=QD GT:AD:DP:GQ:PL 1/1:0,7:7:20:179,20,0 chr1 801142 rs4951928 A T 495.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.99;POSITIVE_TRAIN_SITE;QD=29.82;SOR=0.859;VQSLOD=4.58;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,11:11:36:1|1:801142_A_T:524,36,0 chr1 801143 rs3131974 T C 495.77 PASS AC=2;AF=1.00;AN=2;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=35.44;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=33.74;SOR=0.693;VQSLOD=3.19;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,12:12:36:1|1:801142_A_T:524,36,0 chr1 801702 rs2427926 G C 48.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.202;ClippingRankSum=-1.184e+00;DB;DP=29;ExcessHet=3.0103;FS=8.741;MLEAC=1;MLEAF=0.500;MQ=46.62;MQRankSum=-2.742e+00;NEGATIVE_TRAIN_SITE;QD=1.68;ReadPosRankSum=0.375;SOR=3.014;VQSLOD=-1.601e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:24,5:29:77:77,0,694 chr1 803830 rs2427917 A G 737.77 PASS AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.05;POSITIVE_TRAIN_SITE;QD=30.74;SOR=2.124;VQSLOD=4.94;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,24:24:72:766,72,0 chr1 804046 rs3131973 A G 451.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=46.26;POSITIVE_TRAIN_SITE;QD=30.12;SOR=1.473;VQSLOD=5.98;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,15:15:45:480,45,0 chr1 804148 rs3094317 G A 494.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.56;POSITIVE_TRAIN_SITE;QD=30.92;SOR=0.693;VQSLOD=3.84;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,16:16:48:523,48,0 chr1 805514 rs552659822 AC A 474.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-6.020e-01;ClippingRankSum=-6.650e-01;DB;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.68;MQRankSum=-1.648e+00;POSITIVE_TRAIN_SITE;QD=13.19;ReadPosRankSum=-1.363e+00;SOR=0.616;VQSLOD=2.92;culprit=FS GT:AD:DP:GQ:PL 0/1:17,19:36:99:512,0,445 chr1 806199 rs3115865 T C 196.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.06;NEGATIVE_TRAIN_SITE;QD=24.60;SOR=1.179;VQSLOD=0.298;culprit=QD GT:AD:DP:GQ:PL 1/1:0,8:8:24:225,24,0 chr1 807445 rs191696195 A G 243.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.280e+00;ClippingRankSum=-7.020e-01;DB;DP=21;ExcessHet=3.0103;FS=11.311;MLEAC=1;MLEAF=0.500;MQ=48.41;MQRankSum=0.702;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=12.83;ReadPosRankSum=1.20;SOR=2.447;VQSLOD=0.473;culprit=FS GT:AD:DP:GQ:PL 0/1:8,11:19:99:272,0,216 chr1 807641 rs3964475 T C 148.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.910;ClippingRankSum=0.201;DB;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=33.95;MQRankSum=2.65;POSITIVE_TRAIN_SITE;QD=10.63;ReadPosRankSum=0.201;SOR=0.693;VQSLOD=2.21;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:7,7:14:99:177,0,141 chr1 807692 rs2488505 C A 349.77 PASS AC=2;AF=1.00;AN=2;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=39.43;POSITIVE_TRAIN_SITE;QD=26.91;SOR=1.179;VQSLOD=3.43;culprit=QD GT:AD:DP:GQ:PL 1/1:0,13:13:39:378,39,0 chr1 808924 rs2519055 C T 92.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.02;QD=23.01;SOR=1.609;VQSLOD=1.08;culprit=QD GT:AD:DP:GQ:PL 1/1:0,4:4:12:120,12,0 chr1 810988 rs3925106 C A 50.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.726e+00;ClippingRankSum=-9.110e-01;DB;DP=37;ExcessHet=3.0103;FS=11.409;MLEAC=1;MLEAF=0.500;MQ=46.01;MQRankSum=-3.277e+00;NEGATIVE_TRAIN_SITE;QD=1.37;ReadPosRankSum=0.175;SOR=1.424;VQSLOD=-2.252e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:30,7:37:79:79,0,856 chr1 811066 rs2722509 C G 56.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.338e+00;ClippingRankSum=0.229;DB;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=47.18;MQRankSum=-3.899e+00;QD=1.96;ReadPosRankSum=-9.430e-01;SOR=0.892;VQSLOD=0.803;culprit=QD GT:AD:DP:GQ:PL 0/1:22,7:29:85:85,0,649 chr1 813498 rs2519043 G T 698.77 PASS AC=2;AF=1.00;AN=2;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.28;POSITIVE_TRAIN_SITE;QD=30.38;SOR=1.179;VQSLOD=4.61;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,23:23:69:727,69,0 chr1 813885 rs199734026 G A 78.85 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;ClippingRankSum=0.731;DB;DP=5;ExcessHet=3.0103;FS=6.990;MLEAC=1;MLEAF=0.500;MQ=26.22;MQRankSum=0.731;QD=15.77;ReadPosRankSum=0.731;SOR=3.229;VQSLOD=-3.893e+00;culprit=SOR GT:AD:DP:GQ:PL 0/1:1,4:5:17:107,0,17 chr1 814378 rs4399101 C T 67.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;ClippingRankSum=0.804;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.12;MQRankSum=0.804;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=33.88;ReadPosRankSum=0.804;SOR=0.693;VQSLOD=-1.419e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:1,1:2:44:0|1:814378_C_T:96,0,44 chr1 814380 rs12045157 C G 67.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=-7.270e-01;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.65;MQRankSum=0.727;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=16.94;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=0.486;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 0/1:1,3:4:44:0|1:814378_C_T:96,0,44 chr1 814476 rs12409679 C T 168.79 PASS AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.80;QD=21.10;SOR=1.179;VQSLOD=0.786;culprit=QD GT:AD:DP:GQ:PL 1/1:0,8:8:23:197,23,0 chr1 814583 rs529266287 T TAA 182.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=39.59;POSITIVE_TRAIN_SITE;QD=30.47;SOR=1.329;VQSLOD=5.80;culprit=FS GT:AD:DP:GQ:PL 1/1:0,6:6:18:220,18,0 chr1 814609 rs12409693 C T 181.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=39.71;QD=33.93;SOR=1.981;VQSLOD=3.10;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,5:5:15:1|1:814609_C_T:210,15,0 chr1 814617 rs12410209 A G 152.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.66;QD=33.49;SOR=1.609;VQSLOD=2.31;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,4:4:12:1|1:814609_C_T:180,12,0 chr1 814633 rs12409695 C T 107.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.02;QD=33.07;SOR=1.179;VQSLOD=1.69;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,3:3:9:1|1:814609_C_T:135,9,0 chr1 814673 rs11240770 A C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.53;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=4.70;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:814673_A_C:90,6,0 chr1 814675 rs11240771 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.53;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=4.34;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:814673_A_C:90,6,0 chr1 814962 rs10793768 C T 214.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.65;QD=26.85;SOR=1.863;VQSLOD=1.95;culprit=QD GT:AD:DP:GQ:PL 1/1:0,8:8:24:243,24,0 chr1 816904 . A C 111.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=1.02;ClippingRankSum=-1.016e+00;DP=24;ExcessHet=3.0103;FS=1.810;MLEAC=1;MLEAF=0.500;MQ=52.22;MQRankSum=-3.811e+00;NEGATIVE_TRAIN_SITE;QD=4.66;ReadPosRankSum=0.064;SOR=0.738;VQSLOD=-2.146e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:17,7:24:99:140,0,457 chr1 817186 rs3094315 G A 675.77 PASS AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.58;POSITIVE_TRAIN_SITE;QD=29.38;SOR=0.776;VQSLOD=6.61;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,23:23:68:704,68,0 chr1 817341 rs3131972 A G 868.77 PASS AC=2;AF=1.00;AN=2;DB;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=29.96;SOR=1.071;VQSLOD=21.95;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,29:29:87:897,87,0 chr1 817514 rs3131971 T C 312.77 VQSRTrancheSNP99.80to99.90 AC=2;AF=1.00;AN=2;DB;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.00;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=22.34;SOR=5.421;VQSLOD=-1.540e+00;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,14:14:41:341,41,0 chr1 817889 rs61770172 C G 302.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=46.11;QD=27.52;SOR=1.270;VQSLOD=3.21;culprit=QD GT:AD:DP:GQ:PL 1/1:0,11:11:33:331,33,0 chr1 818025 rs3115860 C A 433.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.41;POSITIVE_TRAIN_SITE;QD=28.92;SOR=1.112;VQSLOD=5.23;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,15:15:44:462,44,0 chr1 818045 rs3131970 T C 535.77 PASS AC=2;AF=1.00;AN=2;DB;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.84;POSITIVE_TRAIN_SITE;QD=29.76;SOR=1.493;VQSLOD=5.06;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,18:18:54:564,54,0 chr1 818094 rs2073814 C G 621.77 PASS AC=2;AF=1.00;AN=2;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.14;POSITIVE_TRAIN_SITE;QD=28.26;SOR=0.874;VQSLOD=5.86;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,22:22:65:650,65,0 chr1 818464 rs59507194 CCT C 232.80 PASS AC=2;AF=1.00;AN=2;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=27.87;QD=32.11;SOR=2.303;VQSLOD=4.30;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 1/1:0,6:6:18:1|1:818464_CCT_C:270,18,0 chr1 818469 rs58324164 G T 241.84 PASS AC=2;AF=1.00;AN=2;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=27.87;QD=26.86;SOR=2.303;VQSLOD=1.30;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,6:6:18:1|1:818464_CCT_C:270,18,0 chr1 818802 rs3131969 A G 1213.77 PASS AC=2;AF=1.00;AN=2;DB;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.16;POSITIVE_TRAIN_SITE;QD=30.35;SOR=1.255;VQSLOD=6.26;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,29:29:87:1|1:818802_A_G:1242,87,0 chr1 818812 rs3131968 A G 1262.77 PASS AC=2;AF=1.00;AN=2;DB;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.73;POSITIVE_TRAIN_SITE;QD=30.97;SOR=1.143;VQSLOD=5.85;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,30:30:93:1|1:818802_A_G:1291,93,0 chr1 818954 rs3131967 T C 790.77 PASS AC=2;AF=1.00;AN=2;DB;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.45;POSITIVE_TRAIN_SITE;QD=29.29;SOR=0.765;VQSLOD=6.44;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,27:27:81:819,81,0 chr1 819123 rs3115859 G A 1018.77 PASS AC=2;AF=1.00;AN=2;DB;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=31.84;SOR=0.693;VQSLOD=22.12;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,32:32:96:1047,96,0 chr1 819584 rs3131966 C T 695.77 PASS AC=2;AF=1.00;AN=2;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.33;POSITIVE_TRAIN_SITE;QD=30.25;SOR=0.963;VQSLOD=5.90;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,23:23:69:724,69,0 chr1 820395 rs3131965 A G 277.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.25;SOR=0.859;VQSLOD=18.26;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,11:11:33:1|1:820395_A_G:306,33,0 chr1 820507 rs3131964 C G 826.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.52;POSITIVE_TRAIN_SITE;QD=29.43;SOR=0.892;VQSLOD=5.66;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,20:20:60:1|1:820507_C_G:855,60,0 chr1 820510 rs3115858 A T 826.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.52;POSITIVE_TRAIN_SITE;QD=28.18;SOR=0.892;VQSLOD=4.27;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,20:20:60:1|1:820507_C_G:855,60,0 chr1 820560 rs3115857 C T 592.77 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.93;ClippingRankSum=0.992;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.71;MQRankSum=1.62;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=24.70;ReadPosRankSum=-1.201e+00;SOR=1.609;VQSLOD=1.26;culprit=QD GT:AD:DP:GQ:PL 1/1:2,22:24:51:621,51,0 chr1 820888 rs12567639 G A 304.96 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-6.680e-01;ClippingRankSum=0.935;DB;DP=13;ExcessHet=3.0103;FS=4.150;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=-1.737e+00;POSITIVE_TRAIN_SITE;QD=23.46;ReadPosRankSum=1.47;SOR=1.250;VQSLOD=15.65;culprit=QD GT:AD:DP:GQ:PL 1/1:1,12:13:5:332,5,0 chr1 820929 rs61768167 T C 112.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.77;ClippingRankSum=-1.663e+00;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.52;MQRankSum=-1.034e+00;QD=10.25;ReadPosRankSum=0.278;SOR=1.270;VQSLOD=1.33;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 0/1:7,4:11:99:0|1:820929_T_C:141,0,326 chr1 820932 rs61768168 T G 106.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.289;ClippingRankSum=0.00;DB;DP=13;ExcessHet=3.0103;FS=2.398;MLEAC=1;MLEAF=0.500;MQ=59.56;MQRankSum=0.00;QD=8.90;ReadPosRankSum=0.00;SOR=1.609;VQSLOD=-2.654e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:8,4:12:99:0|1:820929_T_C:135,0,409 chr1 820933 . C G 112.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.929;ClippingRankSum=0.825;DP=13;ExcessHet=3.0103;FS=2.398;MLEAC=1;MLEAF=0.500;MQ=59.56;MQRankSum=0.289;QD=9.40;ReadPosRankSum=0.00;SOR=1.609;VQSLOD=-2.755e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:8,4:12:99:0|1:820929_T_C:141,0,366 chr1 820937 . C T 109.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.495;ClippingRankSum=-9.190e-01;DP=15;ExcessHet=3.0103;FS=2.363;MLEAC=1;MLEAF=0.500;MQ=59.62;MQRankSum=-3.540e-01;QD=7.84;ReadPosRankSum=0.212;SOR=1.609;VQSLOD=-1.954e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:10,4:14:99:0|1:820929_T_C:138,0,408 chr1 820940 . G T 109.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.20;ClippingRankSum=0.778;DP=16;ExcessHet=3.0103;FS=2.363;MLEAC=1;MLEAF=0.500;MQ=59.64;MQRankSum=-6.360e-01;QD=7.84;ReadPosRankSum=-4.950e-01;SOR=1.609;VQSLOD=-2.445e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:10,4:14:99:0|1:820929_T_C:138,0,408 chr1 820946 . C G 109.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-7.100e-02;ClippingRankSum=-1.061e+00;DP=16;ExcessHet=3.0103;FS=2.363;MLEAC=1;MLEAF=0.500;MQ=59.64;MQRankSum=-1.202e+00;NEGATIVE_TRAIN_SITE;QD=7.84;ReadPosRankSum=-1.485e+00;SOR=1.609;VQSLOD=-5.722e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:10,4:14:99:0|1:820929_T_C:138,0,408 chr1 820948 . T A 109.77 VQSRTrancheSNP99.50to99.60 AC=1;AF=0.500;AN=2;BaseQRankSum=0.423;ClippingRankSum=-7.610e-01;DP=15;ExcessHet=3.0103;FS=6.368;MLEAC=1;MLEAF=0.500;MQ=59.62;MQRankSum=-4.230e-01;NEGATIVE_TRAIN_SITE;QD=8.44;ReadPosRankSum=-1.268e+00;SOR=2.833;VQSLOD=-7.495e-01;culprit=SOR GT:AD:DP:GQ:PGT:PID:PL 0/1:10,3:13:99:0|1:820929_T_C:138,0,408 chr1 820949 . G A 109.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-8.500e-02;ClippingRankSum=-2.540e-01;DP=15;ExcessHet=3.0103;FS=6.368;MLEAC=1;MLEAF=0.500;MQ=59.62;MQRankSum=-1.437e+00;NEGATIVE_TRAIN_SITE;QD=8.44;ReadPosRankSum=-1.606e+00;SOR=2.833;VQSLOD=-1.255e+00;culprit=SOR GT:AD:DP:GQ:PGT:PID:PL 0/1:10,3:13:99:0|1:820929_T_C:138,0,408 chr1 820953 . A C 67.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;ClippingRankSum=0.322;DP=14;ExcessHet=3.0103;FS=3.282;MLEAC=1;MLEAF=0.500;MQ=59.59;MQRankSum=-9.670e-01;NEGATIVE_TRAIN_SITE;QD=5.65;ReadPosRankSum=-2.256e+00;SOR=2.303;VQSLOD=-1.404e+00;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:10,2:12:96:0|1:820929_T_C:96,0,411 chr1 821000 rs3131963 T A 485.77 PASS AC=2;AF=1.00;AN=2;DB;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.68;POSITIVE_TRAIN_SITE;QD=30.36;SOR=0.693;VQSLOD=5.98;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,16:16:48:514,48,0 chr1 821224 rs3131962 A G 384.77 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.52;ClippingRankSum=0.868;DB;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.95;MQRankSum=-1.519e+00;POSITIVE_TRAIN_SITE;QD=24.05;ReadPosRankSum=0.00;SOR=0.275;VQSLOD=2.65;culprit=QD GT:AD:DP:GQ:PL 1/1:1,15:16:37:413,37,0 chr1 822260 rs3115853 G A 320.77 PASS AC=2;AF=1.00;AN=2;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.50;POSITIVE_TRAIN_SITE;QD=26.73;SOR=1.022;VQSLOD=5.37;culprit=QD GT:AD:DP:GQ:PL 1/1:0,12:12:35:349,35,0 chr1 822354 rs4951929 C T 557.77 PASS AC=2;AF=1.00;AN=2;DB;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.19;POSITIVE_TRAIN_SITE;QD=30.99;SOR=0.914;VQSLOD=5.84;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,18:18:54:586,54,0 chr1 822427 rs70949520 CCCTGGCCAGCAGATCCACCCTGTCTATACTACCTG C 253.75 PASS AC=2;AF=1.00;AN=2;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.81;QD=28.32;SOR=2.584;VQSLOD=4.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,7:7:23:291,23,0 chr1 822556 rs4951862 C A 345.90 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=0.935;ClippingRankSum=-6.680e-01;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=-9.350e-01;POSITIVE_TRAIN_SITE;QD=26.61;SOR=2.303;VQSLOD=13.85;culprit=QD GT:AD:DP:GQ:PL 1/1:1,12:13:15:374,15,0 chr1 822764 rs3131956 A G 273.77 PASS AC=2;AF=1.00;AN=2;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=27.38;SOR=1.085;VQSLOD=21.29;culprit=QD GT:AD:DP:GQ:PL 1/1:0,10:10:30:302,30,0 chr1 822944 rs3131955 T C 433.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.30;POSITIVE_TRAIN_SITE;QD=28.92;SOR=1.112;VQSLOD=6.26;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,15:15:44:462,44,0 chr1 823246 rs3131954 C T 500.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.99;POSITIVE_TRAIN_SITE;QD=31.30;SOR=1.244;VQSLOD=6.97;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,16:16:48:529,48,0 chr1 824320 rs3115852 T C 515.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=35.72;QD=30.34;SOR=1.061;VQSLOD=3.54;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,17:17:51:544,51,0 chr1 824457 rs3115851 T A 457.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.65;POSITIVE_TRAIN_SITE;QD=30.52;SOR=0.818;VQSLOD=5.70;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,15:15:45:486,45,0 chr1 825532 rs1048488 C T 860.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.60;POSITIVE_TRAIN_SITE;QD=33.11;SOR=1.445;VQSLOD=6.35;culprit=QD GT:AD:DP:GQ:PL 1/1:0,26:26:78:889,78,0 chr1 825767 rs3115850 T C 961.77 PASS AC=2;AF=1.00;AN=2;DB;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=32.06;SOR=1.329;VQSLOD=21.90;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,30:30:90:1|1:825767_T_C:990,90,0 chr1 826352 rs2286139 C T 487.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=46.73;POSITIVE_TRAIN_SITE;QD=32.52;SOR=2.448;VQSLOD=5.17;culprit=QD GT:AD:DP:GQ:PL 1/1:0,15:15:45:516,45,0 chr1 826372 rs1057213 C T 324.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.95;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=29.52;SOR=4.977;VQSLOD=2.03;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,11:11:33:353,33,0 chr1 826420 rs1064272 A T 175.84 PASS AC=2;AF=1.00;AN=2;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.61;POSITIVE_TRAIN_SITE;QD=29.31;SOR=2.303;VQSLOD=4.14;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,6:6:18:204,18,0 chr1 826431 rs1057212 G A 239.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.49;QD=29.97;SOR=1.863;VQSLOD=2.21;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,8:8:24:268,24,0 chr1 826577 rs59038458 A AT 326.74 PASS AC=2;AF=1.00;AN=2;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=39.78;POSITIVE_TRAIN_SITE;QD=29.65;SOR=2.093;VQSLOD=5.93;culprit=FS GT:AD:DP:GQ:PL 1/1:0,9:9:27:364,27,0 chr1 826893 rs3115849 G A 764.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.24;POSITIVE_TRAIN_SITE;QD=29.41;SOR=1.445;VQSLOD=4.76;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,26:26:77:793,77,0 chr1 827209 rs3115848 G C 1186.77 PASS AC=2;AF=1.00;AN=2;DB;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.78;POSITIVE_TRAIN_SITE;QD=35.03;SOR=0.765;VQSLOD=5.85;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,27:27:81:1|1:827209_G_C:1215,81,0 chr1 827212 rs3131950 C G 1186.77 PASS AC=2;AF=1.00;AN=2;DB;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.78;POSITIVE_TRAIN_SITE;QD=25.82;SOR=0.765;VQSLOD=4.55;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,27:27:81:1|1:827209_G_C:1215,81,0 chr1 827221 rs3131949 T C 1210.77 PASS AC=2;AF=1.00;AN=2;DB;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.62;POSITIVE_TRAIN_SITE;QD=32.17;SOR=0.693;VQSLOD=5.35;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,28:28:84:1|1:827209_G_C:1239,84,0 chr1 827252 rs3131948 T A 762.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.98;POSITIVE_TRAIN_SITE;QD=29.34;SOR=0.846;VQSLOD=5.64;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,26:26:77:791,77,0 chr1 828014 rs3115847 G A 195.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.27;ClippingRankSum=0.898;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=28.86;MQRankSum=1.27;POSITIVE_TRAIN_SITE;QD=19.58;ReadPosRankSum=-4.800e-01;SOR=0.473;VQSLOD=1.49;culprit=QD GT:AD:DP:GQ:PL 0/1:2,8:10:29:224,0,29 chr1 828389 rs372986968 A AT 522.73 PASS AC=2;AF=1.00;AN=2;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.90;QD=24.89;SOR=0.784;VQSLOD=5.04;culprit=FS GT:AD:DP:GQ:PL 1/1:0,21:21:63:560,63,0 chr1 830725 rs2519015 T A 648.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=39.45;POSITIVE_TRAIN_SITE;QD=32.44;SOR=0.693;VQSLOD=5.41;culprit=QD GT:AD:DP:GQ:PL 1/1:0,20:20:60:677,60,0 chr1 832400 rs2905042 G A 780.77 PASS AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.55;POSITIVE_TRAIN_SITE;QD=31.23;SOR=0.770;VQSLOD=5.70;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,25:25:75:809,75,0 chr1 832736 rs376645387 A AGTTTT 223.82 PASS AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=32.77;SOR=1.329;VQSLOD=7.43;culprit=FS GT:AD:DP:GQ:PL 1/1:0,6:6:17:261,17,0 chr1 832873 rs2977608 A C 523.77 PASS AC=2;AF=1.00;AN=2;DB;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.07;POSITIVE_TRAIN_SITE;QD=27.57;SOR=1.609;VQSLOD=6.09;culprit=QD GT:AD:DP:GQ:PL 1/1:0,19:19:56:552,56,0 chr1 834449 rs2977607 C A 603.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.74;POSITIVE_TRAIN_SITE;QD=30.19;SOR=1.127;VQSLOD=5.54;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,20:20:59:632,59,0 chr1 834695 rs2977606 C T 488.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.06;POSITIVE_TRAIN_SITE;QD=30.55;SOR=0.941;VQSLOD=5.00;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,16:16:48:517,48,0 chr1 835538 rs3095826 T G 306.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=30.67;QD=27.89;SOR=0.859;VQSLOD=3.08;culprit=QD GT:AD:DP:GQ:PL 1/1:0,11:11:33:335,33,0 chr1 836030 rs2519006 C T 715.77 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-7.630e-01;ClippingRankSum=1.04;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=39.16;MQRankSum=1.60;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=28.63;ReadPosRankSum=-1.179e+00;SOR=0.382;VQSLOD=1.45;culprit=MQ GT:AD:DP:GQ:PL 1/1:1,24:25:49:744,49,0 chr1 836443 rs2977605 T C 525.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.00;POSITIVE_TRAIN_SITE;QD=26.29;SOR=1.127;VQSLOD=4.24;culprit=QD GT:AD:DP:GQ:PL 1/1:0,20:20:59:554,59,0 chr1 837375 rs2905039 A C 699.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.33;POSITIVE_TRAIN_SITE;QD=26.91;SOR=0.846;VQSLOD=5.90;culprit=QD GT:AD:DP:GQ:PL 1/1:0,26:26:77:728,77,0 chr1 839356 rs28830877 A C 100.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.68;POSITIVE_TRAIN_SITE;QD=25.01;SOR=1.609;VQSLOD=4.66;culprit=QD GT:AD:DP:GQ:PL 1/1:0,4:4:12:128,12,0 chr1 839480 rs747980890 CACACACCTGGACAA C 87.25 PASS AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=31.32;QD=30.77;SOR=2.303;VQSLOD=3.78;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:9:1|1:839480_CACACACCTGGACAA_C:124,9,0 chr1 839515 rs778519663 CTAGACACACACACCTGGACACACACACG C 154.87 PASS AC=2;AF=1.00;AN=2;DB;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.52;QD=30.97;SOR=1.022;VQSLOD=3.10;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 1/1:0,5:5:15:1|1:839480_CACACACCTGGACAA_C:192,15,0 chr1 840046 rs2905037 G A 476.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.07;POSITIVE_TRAIN_SITE;QD=29.80;SOR=1.244;VQSLOD=5.90;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,16:16:48:505,48,0 chr1 840279 rs2905035 A G 453.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.07;POSITIVE_TRAIN_SITE;QD=30.25;SOR=0.818;VQSLOD=6.41;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,15:15:45:482,45,0 chr1 840409 rs757138879 TA T 228.73 PASS AC=2;AF=1.00;AN=2;DB;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.41;POSITIVE_TRAIN_SITE;QD=20.79;SOR=0.859;VQSLOD=5.36;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 1/1:0,11:11:33:1|1:840409_TA_T:266,33,0 chr1 841166 rs12124819 A G 234.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.100e-02;ClippingRankSum=0.713;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.651;POSITIVE_TRAIN_SITE;QD=10.21;ReadPosRankSum=0.651;SOR=0.569;VQSLOD=16.95;culprit=MQ GT:AD:DP:GQ:PL 0/1:13,10:23:99:263,0,355 chr1 841742 rs2980319 A T 809.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=31.14;SOR=0.846;VQSLOD=20.42;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,26:26:78:838,78,0 chr1 842922 rs112119688 C CCT 698.73 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.56;POSITIVE_TRAIN_SITE;QD=28.07;SOR=0.804;VQSLOD=6.35;culprit=FS GT:AD:DP:GQ:PL 1/1:0,17:17:51:736,51,0 chr1 843189 rs2977615 A G 567.77 PASS AC=2;AF=1.00;AN=2;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.24;POSITIVE_TRAIN_SITE;QD=27.04;SOR=0.784;VQSLOD=5.95;culprit=QD GT:AD:DP:GQ:PL 1/1:0,21:21:62:596,62,0 chr1 844647 rs2977613 G T 764.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.21;POSITIVE_TRAIN_SITE;QD=29.41;SOR=1.697;VQSLOD=5.81;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,26:26:77:793,77,0 chr1 845405 rs2977612 T A 1056.77 PASS AC=2;AF=1.00;AN=2;DB;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.78;POSITIVE_TRAIN_SITE;QD=32.02;SOR=0.752;VQSLOD=6.04;culprit=QD GT:AD:DP:GQ:PL 1/1:0,33:33:99:1085,99,0 chr1 847924 rs2980295 T C 944.77 PASS AC=2;AF=1.00;AN=2;DB;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.50;POSITIVE_TRAIN_SITE;QD=31.49;SOR=0.826;VQSLOD=4.58;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,30:30:90:973,90,0 chr1 849670 rs2905062 G A 676.77 PASS AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=27.07;SOR=1.136;VQSLOD=21.27;culprit=QD GT:AD:DP:GQ:PL 1/1:0,25:25:72:705,72,0 chr1 850609 rs2980300 T C 468.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.77;POSITIVE_TRAIN_SITE;QD=27.57;SOR=1.061;VQSLOD=5.43;culprit=QD GT:AD:DP:GQ:PL 1/1:0,17:17:50:497,50,0 chr1 850867 rs59319764 G A 256.78 PASS AC=2;AF=1.00;AN=2;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.35;QD=28.53;SOR=2.093;VQSLOD=3.69;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,9:9:27:285,27,0 chr1 851430 rs2905061 G A 110.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.00;POSITIVE_TRAIN_SITE;QD=27.51;SOR=1.609;VQSLOD=4.00;culprit=QD GT:AD:DP:GQ:PL 1/1:0,4:4:12:138,12,0 chr1 851639 rs2905060 C T 74.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.33;QD=18.51;SOR=0.693;VQSLOD=0.166;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,4:4:12:102,12,0 chr1 851755 rs28753393 A G 226.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=38.49;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=28.35;SOR=4.407;VQSLOD=1.55;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,8:8:24:255,24,0 chr1 851805 rs2905058 G A 370.77 PASS AC=2;AF=1.00;AN=2;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=38.28;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=30.90;SOR=5.136;VQSLOD=0.368;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,12:12:36:399,36,0 chr1 851825 rs2905057 G A 355.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=39.29;POSITIVE_TRAIN_SITE;QD=32.34;SOR=3.442;VQSLOD=3.64;culprit=QD GT:AD:DP:GQ:PL 1/1:0,11:11:33:384,33,0 chr1 851882 rs2905056 C G 373.77 PASS AC=2;AF=1.00;AN=2;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.87;POSITIVE_TRAIN_SITE;QD=31.15;SOR=2.670;VQSLOD=4.86;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,12:12:36:402,36,0 chr1 852019 rs2905055 G T 806.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.96;POSITIVE_TRAIN_SITE;QD=31.03;SOR=0.846;VQSLOD=6.35;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,26:26:78:835,78,0 chr1 852047 rs187283089 C T 227.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.88;ClippingRankSum=0.713;DB;DP=24;ExcessHet=3.0103;FS=19.109;MLEAC=1;MLEAF=0.500;MQ=58.87;MQRankSum=-7.130e-01;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=9.90;ReadPosRankSum=0.899;SOR=2.212;VQSLOD=-1.000e-04;culprit=FS GT:AD:DP:GQ:PL 0/1:13,10:23:99:256,0,299 chr1 852305 rs2905054 G T 894.77 PASS AC=2;AF=1.00;AN=2;DB;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.74;POSITIVE_TRAIN_SITE;QD=31.96;SOR=0.997;VQSLOD=5.86;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,28:28:84:923,84,0 chr1 852464 rs2905053 C T 748.77 PASS AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=42.90;POSITIVE_TRAIN_SITE;QD=31.20;SOR=0.859;VQSLOD=4.60;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,24:24:72:777,72,0 chr1 853333 rs2980306 T C 632.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.22;POSITIVE_TRAIN_SITE;QD=31.64;SOR=1.721;VQSLOD=5.37;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,20:20:60:661,60,0 chr1 853460 rs10157303 T C 123.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.610e-01;ClippingRankSum=0.00;DB;DP=10;ExcessHet=3.0103;FS=2.808;MLEAC=1;MLEAF=0.500;MQ=36.41;MQRankSum=-7.290e-01;NEGATIVE_TRAIN_SITE;QD=13.75;ReadPosRankSum=-3.610e-01;SOR=1.981;VQSLOD=-1.961e+00;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:4,5:9:99:0|1:853460_T_C:152,0,164 chr1 853464 rs10159337 C G 101.77 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=1.37;ClippingRankSum=-9.220e-01;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.74;MQRankSum=-4.210e-01;NEGATIVE_TRAIN_SITE;QD=12.72;ReadPosRankSum=0.922;SOR=1.609;VQSLOD=-8.499e-01;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:4,4:8:99:0|1:853460_T_C:130,0,167 chr1 853719 rs10158938 G A 167.84 PASS AC=2;AF=1.00;AN=2;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.35;NEGATIVE_TRAIN_SITE;QD=27.97;SOR=3.912;VQSLOD=1.52;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,6:6:18:196,18,0 chr1 855316 rs76089329 C CAT 1028.73 PASS AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=27.93;SOR=1.519;VQSLOD=5.62;culprit=FS GT:AD:DP:GQ:PL 1/1:0,24:24:72:1066,72,0 chr1 855378 rs72558500 GTA G 817.73 PASS AC=2;AF=1.00;AN=2;DB;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.91;SOR=1.292;VQSLOD=4.26;culprit=FS GT:AD:DP:GQ:PL 1/1:0,19:19:57:855,57,0 chr1 856883 rs1044922 A G 779.77 PASS AC=2;AF=1.00;AN=2;DB;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.25;POSITIVE_TRAIN_SITE;QD=27.85;SOR=1.179;VQSLOD=4.42;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,28:28:83:808,83,0 chr1 857100 rs2905036 C T 726.77 PASS AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.84;POSITIVE_TRAIN_SITE;QD=30.28;SOR=1.802;VQSLOD=5.84;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,24:24:72:755,72,0 chr1 858049 rs2519067 T C 427.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.20;POSITIVE_TRAIN_SITE;QD=28.52;SOR=1.911;VQSLOD=5.17;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,15:15:45:456,45,0 chr1 860178 . C CTTTTT 53.70 PASS AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.00;SOR=0.693;VQSLOD=3.26;culprit=FS GT:AD:DP:GQ:PL 1/1:0,0:0:6:90,6,0 chr1 861154 rs72631879 T C 33.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.298e+00;ClippingRankSum=1.01;DB;DP=37;ExcessHet=3.0103;FS=3.928;MLEAC=1;MLEAF=0.500;MQ=46.50;MQRankSum=-2.740e+00;NEGATIVE_TRAIN_SITE;QD=0.91;ReadPosRankSum=0.515;SOR=1.245;VQSLOD=-1.736e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:31,6:37:62:62,0,868 chr1 861347 rs2909612 G T 511.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=35.65;QD=30.10;SOR=1.061;VQSLOD=3.68;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,17:17:51:540,51,0 chr1 861387 rs12076540 G A 669.78 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.491;ClippingRankSum=0.045;DB;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=36.91;MQRankSum=0.223;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=23.92;ReadPosRankSum=1.12;SOR=0.846;VQSLOD=1.62;culprit=QD GT:AD:DP:GQ:PL 0/1:2,26:28:0:695,0,0 chr1 861940 rs367950410 C G 31.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=1.07;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.47;MQRankSum=-1.067e+00;QD=3.97;ReadPosRankSum=0.572;SOR=0.307;VQSLOD=0.955;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:6,2:8:60:0|1:861914_A_AGAG:60,0,604 chr1 862646 rs4951864 C T 797.77 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.60;ClippingRankSum=-1.467e+00;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.35;MQRankSum=-2.670e-01;POSITIVE_TRAIN_SITE;QD=30.68;ReadPosRankSum=-9.330e-01;SOR=0.255;VQSLOD=2.93;culprit=MQ GT:AD:DP:GQ:PL 1/1:1,25:26:68:826,68,0 chr1 864083 rs4245756 T C 1062.77 PASS AC=2;AF=1.00;AN=2;DB;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=31.26;SOR=0.811;VQSLOD=22.00;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,34:34:99:1091,101,0 chr1 864627 rs6681049 T C 612.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.36;POSITIVE_TRAIN_SITE;QD=30.64;SOR=1.402;VQSLOD=4.92;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,20:20:60:641,60,0 chr1 865003 rs4951931 C T 712.77 PASS AC=2;AF=1.00;AN=2;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.98;POSITIVE_TRAIN_SITE;QD=30.99;SOR=1.179;VQSLOD=5.18;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,23:23:68:741,68,0 chr1 866563 rs7516866 C T 568.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.36;POSITIVE_TRAIN_SITE;QD=26.83;SOR=0.941;VQSLOD=5.08;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,16:16:48:1|1:866563_C_T:597,48,0 chr1 866626 rs9700144 T C 322.89 VQSRTrancheSNP99.60to99.80 AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=-6.960e-01;DB;DP=10;ExcessHet=3.0103;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=49.57;MQRankSum=1.39;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=32.29;ReadPosRankSum=-1.044e+00;SOR=1.198;VQSLOD=-8.698e-01;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 0/1:1,9:10:2:0|1:866563_C_T:349,0,2 chr1 866940 rs12565310 G A 138.10 VQSRTrancheSNP99.80to99.90 AC=2;AF=1.00;AN=2;BaseQRankSum=0.742;ClippingRankSum=-7.420e-01;DB;DP=7;ExcessHet=3.0103;FS=5.441;MLEAC=2;MLEAF=1.00;MQ=52.34;MQRankSum=0.742;NEGATIVE_TRAIN_SITE;QD=19.73;ReadPosRankSum=-7.420e-01;SOR=2.225;VQSLOD=-1.348e+00;culprit=MQ GT:AD:DP:GQ:PL 1/1:1,6:7:11:166,11,0 chr1 868735 rs9725068 G A 606.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.26;POSITIVE_TRAIN_SITE;QD=30.34;SOR=1.721;VQSLOD=4.42;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,20:20:59:635,59,0 chr1 869160 rs11240778 T C 734.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=28.26;SOR=1.022;VQSLOD=21.96;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,26:26:78:763,78,0 chr1 871922 rs140363434 A AT 280.73 PASS AC=2;AF=1.00;AN=2;DB;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=21.59;SOR=2.147;VQSLOD=4.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,13:13:39:318,39,0 chr1 872843 rs4951933 G C 352.77 PASS AC=2;AF=1.00;AN=2;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.43;POSITIVE_TRAIN_SITE;QD=27.14;SOR=0.836;VQSLOD=4.96;culprit=QD GT:AD:DP:GQ:PL 1/1:0,13:13:39:381,39,0 chr1 873251 rs11240779 G A 721.77 PASS AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.38;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.770;VQSLOD=6.47;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,25:25:73:750,73,0 chr1 873542 rs6594027 G A 986.77 PASS AC=2;AF=1.00;AN=2;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.34;POSITIVE_TRAIN_SITE;QD=30.42;SOR=0.776;VQSLOD=6.71;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,23:23:69:1|1:873542_G_A:1015,69,0 chr1 873548 rs11240780 C T 986.77 PASS AC=2;AF=1.00;AN=2;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.76;POSITIVE_TRAIN_SITE;QD=24.50;SOR=0.874;VQSLOD=4.23;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,22:22:69:1|1:873542_G_A:1015,69,0 chr1 875910 rs797008946 G GCCCACGCTCC 218.80 PASS AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.68;QD=29.65;SOR=3.912;VQSLOD=4.45;culprit=FS GT:AD:DP:GQ:PL 1/1:0,6:6:18:256,18,0 chr1 876887 rs7541694 A G 804.77 PASS AC=2;AF=1.00;AN=2;DB;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=26.83;SOR=0.693;VQSLOD=20.75;culprit=QD GT:AD:DP:GQ:PL 1/1:0,30:30:89:833,89,0 chr1 876904 rs7545373 C G 880.77 PASS AC=2;AF=1.00;AN=2;DB;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=31.46;SOR=0.836;VQSLOD=21.40;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,28:28:84:909,84,0 chr1 877371 rs4246500 T C 450.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=32.20;SOR=2.303;VQSLOD=19.47;culprit=QD GT:AD:DP:GQ:PL 1/1:0,14:14:42:479,42,0 chr1 878260 rs4246499 A G 695.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=42.76;POSITIVE_TRAIN_SITE;QD=27.83;SOR=0.770;VQSLOD=3.15;culprit=QD GT:AD:DP:GQ:PL 1/1:0,25:25:74:724,74,0 chr1 878367 rs4970388 G A 551.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.21;POSITIVE_TRAIN_SITE;QD=32.46;SOR=1.061;VQSLOD=4.96;culprit=QD GT:AD:DP:GQ:PL 1/1:0,17:17:51:580,51,0 chr1 878707 rs199713952 C A 55.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.484;ClippingRankSum=-2.560e-01;DB;DP=32;ExcessHet=3.0103;FS=5.673;MLEAC=1;MLEAF=0.500;MQ=47.76;MQRankSum=-2.080e+00;NEGATIVE_TRAIN_SITE;QD=1.74;ReadPosRankSum=-3.130e-01;SOR=2.749;VQSLOD=-1.605e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:28,4:32:84:84,0,1090 chr1 878714 rs61768235 A G 125.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.100e-01;ClippingRankSum=-5.470e-01;DB;DP=34;ExcessHet=3.0103;FS=1.735;MLEAC=1;MLEAF=0.500;MQ=47.15;MQRankSum=-2.689e+00;NEGATIVE_TRAIN_SITE;QD=3.93;ReadPosRankSum=-1.459e+00;SOR=1.270;VQSLOD=-1.612e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:25,7:32:99:154,0,648 chr1 878725 rs201418719 C T 55.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=2.93;ClippingRankSum=1.23;DB;DP=32;ExcessHet=3.0103;FS=5.673;MLEAC=1;MLEAF=0.500;MQ=46.23;MQRankSum=-1.852e+00;NEGATIVE_TRAIN_SITE;QD=1.74;ReadPosRankSum=0.655;SOR=2.749;VQSLOD=-1.610e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:28,4:32:84:84,0,809 chr1 878767 rs4268301 G C 269.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;ClippingRankSum=0.960;DB;DP=41;ExcessHet=3.0103;FS=17.282;MLEAC=1;MLEAF=0.500;MQ=44.50;MQRankSum=-4.054e+00;NEGATIVE_TRAIN_SITE;QD=6.58;ReadPosRankSum=1.93;SOR=2.637;VQSLOD=-3.155e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:29,12:41:99:298,0,737 chr1 878780 rs200699159 C G 31.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.080e-01;ClippingRankSum=-1.227e+00;DB;DP=39;ExcessHet=3.0103;FS=9.286;MLEAC=1;MLEAF=0.500;MQ=42.81;MQRankSum=-2.106e+00;NEGATIVE_TRAIN_SITE;QD=0.81;ReadPosRankSum=1.32;SOR=3.154;VQSLOD=-2.551e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:35,4:39:60:60,0,1180 chr1 878789 rs376363419 G A 128.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=-8.170e-01;ClippingRankSum=0.683;DB;DP=39;ExcessHet=3.0103;FS=5.821;MLEAC=1;MLEAF=0.500;MQ=41.95;MQRankSum=-2.983e+00;NEGATIVE_TRAIN_SITE;QD=3.30;ReadPosRankSum=0.450;SOR=1.877;VQSLOD=-2.110e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:30,9:39:99:157,0,874 chr1 878793 rs201851918 A T 37.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=1.40;ClippingRankSum=0.071;DB;DP=38;ExcessHet=3.0103;FS=9.457;MLEAC=1;MLEAF=0.500;MQ=40.39;MQRankSum=-1.689e+00;NEGATIVE_TRAIN_SITE;QD=0.99;ReadPosRankSum=-5.470e-01;SOR=3.258;VQSLOD=-2.748e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:34,4:38:66:66,0,1142 chr1 878884 rs4571914 C T 974.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=1.59;ClippingRankSum=0.272;DB;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.59;MQRankSum=2.71;NEGATIVE_TRAIN_SITE;QD=23.21;ReadPosRankSum=-8.000e-02;SOR=0.527;VQSLOD=-1.764e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:8,34:42:75:1003,0,75 chr1 878917 rs72888851 T A 200.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.442;ClippingRankSum=-8.800e-02;DB;DP=37;ExcessHet=3.0103;FS=9.049;MLEAC=1;MLEAF=0.500;MQ=44.99;MQRankSum=-3.593e+00;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=5.43;ReadPosRankSum=1.29;SOR=2.041;VQSLOD=-4.457e-01;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:28,9:37:99:229,0,821 chr1 878991 rs150353320 GTGTT G 952.73 PASS AC=2;AF=1.00;AN=2;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=39.22;POSITIVE_TRAIN_SITE;QD=34.02;SOR=0.874;VQSLOD=6.74;culprit=FS GT:AD:DP:GQ:PL 1/1:0,22:22:66:990,66,0 chr1 879012 rs61768236 C T 122.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.80;ClippingRankSum=-1.380e-01;DB;DP=28;ExcessHet=3.0103;FS=3.891;MLEAC=1;MLEAF=0.500;MQ=44.31;MQRankSum=-4.150e-01;NEGATIVE_TRAIN_SITE;QD=4.55;ReadPosRankSum=-6.920e-01;SOR=1.609;VQSLOD=-1.399e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:20,7:27:99:151,0,547 chr1 879025 rs61768237 T C 119.77 VQSRTrancheSNP99.80to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.000e-02;ClippingRankSum=0.345;DB;DP=34;ExcessHet=3.0103;FS=6.332;MLEAC=1;MLEAF=0.500;MQ=46.56;MQRankSum=-1.766e+00;NEGATIVE_TRAIN_SITE;QD=3.52;ReadPosRankSum=0.273;SOR=1.824;VQSLOD=-1.462e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:26,8:34:99:148,0,722 chr1 879229 rs75814620 A T 230.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.119e+00;ClippingRankSum=-6.330e-01;DB;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.63;MQRankSum=-1.196e+00;QD=7.69;ReadPosRankSum=2.04;SOR=0.446;VQSLOD=0.706;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:22,8:30:99:0|1:879229_A_T:259,0,896 chr1 879231 rs199660488 A C 230.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.524e+00;ClippingRankSum=-1.170e-01;DB;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.63;MQRankSum=0.915;QD=7.69;ReadPosRankSum=1.01;SOR=0.446;VQSLOD=1.43;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 0/1:22,8:30:99:0|1:879229_A_T:259,0,896 chr1 880282 rs4970339 G T 670.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=28.35;SOR=1.244;VQSLOD=20.78;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,16:16:48:1|1:880282_G_T:699,48,0 chr1 880301 rs4970338 G T 645.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=28.36;SOR=1.473;VQSLOD=21.69;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,15:15:45:1|1:880282_G_T:674,45,0 chr1 881302 rs75468428 G A 58.77 VQSRTrancheSNP99.95to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=2.29;ClippingRankSum=0.885;DB;DP=32;ExcessHet=3.0103;FS=15.835;MLEAC=1;MLEAF=0.500;MQ=57.62;MQRankSum=-3.203e+00;NEGATIVE_TRAIN_SITE;QD=1.96;ReadPosRankSum=0.824;SOR=3.231;VQSLOD=-3.349e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:26,4:30:87:87,0,1190 chr1 881356 rs112557229 G T 47.77 VQSRTrancheSNP99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=2.85;ClippingRankSum=0.212;DB;DP=36;ExcessHet=3.0103;FS=4.715;MLEAC=1;MLEAF=0.500;MQ=57.41;MQRankSum=-3.559e+00;NEGATIVE_TRAIN_SITE;QD=1.36;ReadPosRankSum=2.95;SOR=1.950;VQSLOD=-2.664e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:30,5:35:76:76,0,921 chr1 881854 rs4970387 A T 440.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=29.38;SOR=1.112;VQSLOD=20.83;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,15:15:47:469,47,0 chr1 883741 rs200893860 C CAT 668.73 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=33.10;SOR=1.244;VQSLOD=6.96;culprit=FS GT:AD:DP:GQ:PL 1/1:0,16:16:48:706,48,0 chr1 884537 rs6605057 A G 589.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.95;POSITIVE_TRAIN_SITE;QD=29.49;SOR=1.127;VQSLOD=5.77;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,20:20:60:618,60,0 chr1 886224 rs149920886 T TGCCCTTTGGCAGAGCAGGTGTGCTGTGCTG 995.73 PASS AC=2;AF=1.00;AN=2;DB;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=28.92;SOR=0.914;VQSLOD=6.80;culprit=FS GT:AD:DP:GQ:PL 1/1:0,18:18:68:1033,68,0 chr1 886507 rs6677354 A G 1060.77 PASS AC=2;AF=1.00;AN=2;DB;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=32.14;SOR=1.352;VQSLOD=21.76;culprit=QD GT:AD:DP:GQ:PL 1/1:0,33:33:99:1089,99,0 chr1 886546 rs35660652 C G 439.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.21;ClippingRankSum=-1.030e-01;DB;DP=35;ExcessHet=3.0103;FS=1.500;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.068e+00;POSITIVE_TRAIN_SITE;QD=12.93;ReadPosRankSum=-2.760e-01;SOR=1.300;VQSLOD=15.93;culprit=MQ GT:AD:DP:GQ:PL 0/1:17,17:34:99:468,0,451 chr1 886568 rs6671445 T C 1282.77 PASS AC=2;AF=1.00;AN=2;DB;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=34.62;SOR=1.483;VQSLOD=19.14;culprit=QD GT:AD:DP:GQ:PL 1/1:0,35:35:99:1311,105,0 chr1 888125 rs13302980 T C 376.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=25.12;SOR=0.818;VQSLOD=20.17;culprit=QD GT:AD:DP:GQ:PL 1/1:0,15:15:44:405,44,0 chr1 888410 rs143626389 G A 159.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.740e-01;ClippingRankSum=0.521;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.058;POSITIVE_TRAIN_SITE;QD=10.65;ReadPosRankSum=1.68;SOR=1.022;VQSLOD=16.64;culprit=MQ GT:AD:DP:GQ:PL 0/1:8,7:15:99:188,0,231 chr1 889689 rs4475692 G C 747.77 PASS AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.20;POSITIVE_TRAIN_SITE;QD=31.16;SOR=0.859;VQSLOD=6.67;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,24:24:72:776,72,0 chr1 890030 rs13303179 G A 850.77 PASS AC=2;AF=1.00;AN=2;DB;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=31.51;SOR=1.528;VQSLOD=21.92;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,27:27:80:879,80,0 chr1 890174 rs4970337 A G 629.77 PASS AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=25.19;SOR=0.941;VQSLOD=20.29;culprit=QD GT:AD:DP:GQ:PL 1/1:0,25:25:73:658,73,0 chr1 890446 rs369620271 C CA 319.73 PASS AC=2;AF=1.00;AN=2;DB;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.62;POSITIVE_TRAIN_SITE;QD=22.84;SOR=0.693;VQSLOD=5.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,14:14:41:357,41,0 chr1 891887 rs2879698 C T 818.77 PASS AC=2;AF=1.00;AN=2;DB;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=26.88;SOR=1.292;VQSLOD=20.50;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,19:19:60:1|1:891887_C_T:847,60,0 chr1 891897 rs4246498 T C 794.77 PASS AC=2;AF=1.00;AN=2;DB;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=29.64;SOR=1.292;VQSLOD=21.80;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,19:19:57:1|1:891887_C_T:823,57,0 chr1 891943 rs4970386 C T 703.77 PASS AC=2;AF=1.00;AN=2;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=31.99;SOR=1.329;VQSLOD=22.14;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,22:22:66:732,66,0 chr1 893787 rs377185360 AAAAAAAAAAAAAAAATATATATATATATATATATAT A 406.73 VQSRTrancheINDEL99.50to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.251;ClippingRankSum=-2.060e+00;DB;DP=19;ExcessHet=3.0103;FS=17.561;MLEAC=1;MLEAF=0.500;MQ=59.12;MQRankSum=0.553;NEGATIVE_TRAIN_SITE;QD=23.93;ReadPosRankSum=1.59;SOR=0.948;VQSLOD=-9.260e-01;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 0/1:6,11:17:99:0|1:893787_AAAAAAAAAAAAAAAATATATATATATATATATATAT_A:444,0,206 chr1 893791 rs544798311 AAAAAAAAAAAATATATATATATATATATATATATAT A 168.73 VQSRTrancheINDEL96.00to97.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.76;ClippingRankSum=0.452;DB;DP=18;ExcessHet=3.0103;FS=14.622;MLEAC=1;MLEAF=0.500;MQ=59.07;MQRankSum=-6.530e-01;POSITIVE_TRAIN_SITE;QD=9.93;ReadPosRankSum=-5.000e-02;SOR=3.900;VQSLOD=0.862;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 0/1:11,6:17:99:1|0:893787_AAAAAAAAAAAAAAAATATATATATATATATATATAT_A:206,0,444 chr1 893953 rs9778019 G A 529.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=31.16;SOR=2.179;VQSLOD=20.26;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,17:17:51:558,51,0 chr1 894257 rs4437820 C T 1093.77 PASS AC=2;AF=1.00;AN=2;DB;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.91;POSITIVE_TRAIN_SITE;QD=31.25;SOR=0.869;VQSLOD=4.59;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,35:35:99:1122,105,0 chr1 894801 rs28444699 A G 741.77 PASS AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.69;POSITIVE_TRAIN_SITE;QD=32.25;SOR=0.776;VQSLOD=6.67;culprit=QD GT:AD:DP:GQ:PL 1/1:0,23:23:69:770,69,0 chr1 895427 rs6422669 G C 700.77 PASS AC=2;AF=1.00;AN=2;DB;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=33.37;SOR=1.230;VQSLOD=21.28;culprit=QD GT:AD:DP:GQ:PL 1/1:0,21:21:63:729,63,0 chr1 896109 rs4970385 C T 912.77 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.08;ClippingRankSum=1.52;DB;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.63;MQRankSum=1.63;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=28.52;ReadPosRankSum=-3.250e-01;SOR=0.321;VQSLOD=2.60;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:1,31:32:50:1|1:896084_G_A:941,50,0 chr1 896529 rs9697642 C T 521.77 PASS AC=2;AF=1.00;AN=2;DB;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=28.99;SOR=1.179;VQSLOD=22.23;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,18:18:53:550,53,0 chr1 896680 rs9697378 G A 1000.77 PASS AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.88;POSITIVE_TRAIN_SITE;QD=30.99;SOR=0.693;VQSLOD=6.28;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,24:24:72:1|1:896680_G_A:1029,72,0 chr1 896686 rs9697380 G C 950.77 PASS AC=2;AF=1.00;AN=2;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.87;POSITIVE_TRAIN_SITE;QD=28.90;SOR=0.874;VQSLOD=6.26;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,22:22:69:1|1:896680_G_A:979,69,0 chr1 896732 rs9697725 T C 528.77 PASS AC=2;AF=1.00;AN=2;DB;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;POSITIVE_TRAIN_SITE;QD=29.38;SOR=0.914;VQSLOD=6.64;culprit=FS GT:AD:DP:GQ:PL 1/1:0,18:18:54:557,54,0 chr1 896798 rs13302934 A G 673.77 PASS AC=2;AF=1.00;AN=2;DB;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.04;POSITIVE_TRAIN_SITE;QD=32.08;SOR=0.990;VQSLOD=6.96;culprit=QD GT:AD:DP:GQ:PL 1/1:0,21:21:63:702,63,0 chr1 896917 rs34017275 CTG C 817.73 PASS AC=2;AF=1.00;AN=2;DB;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=31.47;SOR=1.609;VQSLOD=6.04;culprit=FS GT:AD:DP:GQ:PL 1/1:0,19:19:57:855,57,0 chr1 896938 rs4500250 C A 596.77 PASS AC=2;AF=1.00;AN=2;DB;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=33.15;SOR=0.914;VQSLOD=22.01;culprit=QD GT:AD:DP:GQ:PL 1/1:0,18:18:54:625,54,0 chr1 897018 rs4553118 T C 787.77 PASS AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.55;POSITIVE_TRAIN_SITE;QD=32.82;SOR=1.270;VQSLOD=6.20;culprit=QD GT:AD:DP:GQ:PL 1/1:0,24:24:72:816,72,0 chr1 901834 rs72631888 G C 186.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.990;ClippingRankSum=0.307;DB;DP=22;ExcessHet=3.0103;FS=1.875;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-9.900e-01;POSITIVE_TRAIN_SITE;QD=8.49;ReadPosRankSum=-1.536e+00;SOR=1.457;VQSLOD=16.06;culprit=MQ GT:AD:DP:GQ:PL 0/1:14,8:22:99:215,0,351 chr1 902773 rs35084403 CA C 479.73 PASS AC=2;AF=1.00;AN=2;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=23.99;SOR=0.892;VQSLOD=4.70;culprit=FS GT:AD:DP:GQ:PL 1/1:0,20:20:60:517,60,0 chr1 907236 rs111389427 TA T 71.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.800e-01;ClippingRankSum=-1.139e+00;DB;DP=18;ExcessHet=3.0103;FS=2.158;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.054;POSITIVE_TRAIN_SITE;QD=4.48;ReadPosRankSum=-1.898e+00;SOR=1.190;VQSLOD=3.30;culprit=QD GT:AD:DP:GQ:PL 0/1:10,6:16:99:109,0,213 chr1 907445 rs7519340 A G 495.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=29.16;SOR=1.061;VQSLOD=22.79;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,17:17:51:524,51,0 chr1 908025 rs11516185 A G 257.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.407e+00;ClippingRankSum=0.297;DB;DP=23;ExcessHet=3.0103;FS=4.075;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.231;POSITIVE_TRAIN_SITE;QD=11.72;ReadPosRankSum=0.033;SOR=1.322;VQSLOD=16.71;culprit=MQ GT:AD:DP:GQ:PL 0/1:10,12:22:99:286,0,284 chr1 908690 . A AGAGGGGACAAGTGG 53.70 PASS AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.00;QD=26.85;SOR=2.303;VQSLOD=3.11;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 chr1 909903 rs7366404 G T 406.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.28;POSITIVE_TRAIN_SITE;QD=29.05;SOR=2.303;VQSLOD=4.86;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,14:14:42:435,42,0 chr1 910958 rs4970334 A G 806.77 PASS AC=2;AF=1.00;AN=2;DB;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=28.81;SOR=0.836;VQSLOD=21.97;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,28:28:84:835,84,0 chr1 911109 rs4970333 T C 491.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=30.74;SOR=1.609;VQSLOD=21.89;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,16:16:48:520,48,0 chr1 911220 rs35331099 CT C 824.73 PASS AC=2;AF=1.00;AN=2;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=28.56;SOR=1.179;VQSLOD=7.37;culprit=FS GT:AD:DP:GQ:PL 1/1:0,23:23:69:862,69,0 chr1 911870 rs7416129 G A 832.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=32.03;SOR=1.022;VQSLOD=22.53;culprit=QD GT:AD:DP:GQ:PL 1/1:0,26:26:78:861,78,0 chr1 914618 rs13303222 A G 507.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=31.74;SOR=1.609;VQSLOD=22.30;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,16:16:48:536,48,0 chr1 914838 rs6664536 T A 390.77 PASS AC=2;AF=1.00;AN=2;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=30.06;SOR=0.836;VQSLOD=21.42;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,13:13:39:419,39,0 chr1 914991 rs6679046 G T 300.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=27.34;SOR=1.270;VQSLOD=21.54;culprit=QD GT:AD:DP:GQ:PL 1/1:0,11:11:32:329,32,0 chr1 915400 rs6657440 C T 643.77 PASS AC=2;AF=1.00;AN=2;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=29.26;SOR=0.874;VQSLOD=22.16;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,22:22:66:672,66,0 chr1 916010 rs72631889 G T 173.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.540e-01;ClippingRankSum=0.212;DB;DP=29;ExcessHet=3.0103;FS=1.623;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-5.890e-01;POSITIVE_TRAIN_SITE;QD=5.99;ReadPosRankSum=-4.010e-01;SOR=0.652;VQSLOD=16.47;culprit=QD GT:AD:DP:GQ:PL 0/1:20,9:29:99:202,0,590 chr1 916119 rs4970465 A G 765.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=29.45;SOR=1.220;VQSLOD=22.16;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,26:26:78:794,78,0 chr1 916377 rs4970464 A G 795.77 PASS AC=2;AF=1.00;AN=2;DB;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=27.44;SOR=0.906;VQSLOD=21.28;culprit=QD GT:AD:DP:GQ:PL 1/1:0,29:29:86:824,86,0 chr1 916657 rs4970463 G A 908.77 PASS AC=2;AF=1.00;AN=2;DB;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=32.46;SOR=1.609;VQSLOD=21.90;culprit=QD GT:AD:DP:GQ:PL 1/1:0,28:28:84:937,84,0 chr1 916683 rs28436996 G A 943.77 PASS AC=2;AF=1.00;AN=2;DB;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=31.46;SOR=1.329;VQSLOD=22.62;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,30:30:89:972,89,0 chr1 916753 rs7518702 C T 619.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=30.99;SOR=0.892;VQSLOD=21.66;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,20:20:60:648,60,0 chr1 917495 rs13303369 C T 580.77 PASS AC=2;AF=1.00;AN=2;DB;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=32.26;SOR=1.179;VQSLOD=22.27;culprit=QD GT:AD:DP:GQ:PL 1/1:0,18:18:54:609,54,0 chr1 917584 rs4970461 T G 736.77 PASS AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=29.47;SOR=0.770;VQSLOD=21.89;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,25:25:75:765,75,0 chr1 918574 rs1806509 C A 698.77 PASS AC=2;AF=1.00;AN=2;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=31.76;SOR=0.693;VQSLOD=22.59;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,22:22:66:727,66,0 chr1 919397 rs13303019 A G 532.77 PASS AC=2;AF=1.00;AN=2;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=24.22;SOR=0.874;VQSLOD=17.95;culprit=QD GT:AD:DP:GQ:PL 1/1:0,22:22:64:561,64,0 chr1 919598 rs13303057 A C 561.77 PASS AC=2;AF=1.00;AN=2;DB;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=29.57;SOR=0.793;VQSLOD=21.68;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,19:19:57:590,57,0 chr1 919695 rs6673914 C G 712.77 PASS AC=2;AF=1.00;AN=2;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=32.40;SOR=1.329;VQSLOD=21.94;culprit=QD GT:AD:DP:GQ:PL 1/1:0,22:22:66:741,66,0 chr1 922348 rs6689107 T G 796.77 PASS AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=33.20;SOR=0.693;VQSLOD=21.75;culprit=QD GT:AD:DP:GQ:PL 1/1:0,24:24:72:825,72,0 chr1 923311 rs34628185 TG T 948.73 PASS AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=29.84;SOR=1.358;VQSLOD=6.42;culprit=DP GT:AD:DP:GQ:PL 1/1:0,25:25:75:986,75,0 chr1 923421 rs7418179 A G 1188.77 PASS AC=2;AF=1.00;AN=2;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=32.13;SOR=0.984;VQSLOD=20.55;culprit=DP GT:AD:DP:GQ:PL 1/1:0,37:37:99:1217,111,0 chr1 924024 rs71509444 C G 129.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=25.98;SOR=1.022;VQSLOD=20.14;culprit=QD GT:AD:DP:GQ:PL 1/1:0,5:5:15:158,15,0 chr1 924310 rs71509445 C G 369.77 PASS AC=2;AF=1.00;AN=2;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=28.44;SOR=0.836;VQSLOD=21.03;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,13:13:39:398,39,0 chr1 924321 rs71509446 C G 396.77 PASS AC=2;AF=1.00;AN=2;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=30.52;SOR=0.836;VQSLOD=21.57;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,13:13:39:425,39,0 chr1 924533 rs112703963 A G 294.77 PASS AC=2;AF=1.00;AN=2;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=24.56;SOR=1.022;VQSLOD=19.87;culprit=QD GT:AD:DP:GQ:PL 1/1:0,12:12:35:323,35,0 chr1 925036 rs61464428 G A 608.77 PASS AC=2;AF=1.00;AN=2;DB;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=33.82;SOR=1.493;VQSLOD=20.53;culprit=QD GT:AD:DP:GQ:PL 1/1:0,18:18:54:637,54,0 chr1 925081 rs57465118 G A 496.77 PASS AC=2;AF=1.00;AN=2;DB;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=26.15;SOR=1.022;VQSLOD=19.10;culprit=QD GT:AD:DP:GQ:PL 1/1:0,19:19:56:525,56,0 chr1 925141 rs57924093 C A 536.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=26.84;SOR=0.693;VQSLOD=20.40;culprit=QD GT:AD:DP:GQ:PL 1/1:0,20:20:59:565,59,0 chr1 925308 rs60837925 G A 179.79 PASS AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=22.47;SOR=1.179;VQSLOD=17.93;culprit=QD GT:AD:DP:GQ:PL 1/1:0,8:8:23:208,23,0 chr1 925398 rs61338526 A G 456.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.04;SOR=0.859;VQSLOD=18.74;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,11:11:33:1|1:925398_A_G:485,33,0 chr1 925408 rs773119229 TTGG T 412.74 PASS AC=2;AF=1.00;AN=2;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=29.30;SOR=1.085;VQSLOD=6.19;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 1/1:0,10:10:30:1|1:925398_A_G:450,30,0 chr1 925412 rs200244572 CGCCTGCG C 412.74 PASS AC=2;AF=1.00;AN=2;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.97;SOR=1.085;VQSLOD=5.00;culprit=FS GT:AD:DP:GQ:PGT:PID:PL 1/1:0,10:10:30:1|1:925398_A_G:450,30,0 chr1 925474 rs57816555 T C 267.77 PASS AC=2;AF=1.00;AN=2;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=26.78;SOR=1.609;VQSLOD=21.02;culprit=QD GT:AD:DP:GQ:PL 1/1:0,10:10:30:296,30,0 chr1 925628 rs28521172 G C 650.77 PASS AC=2;AF=1.00;AN=2;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=28.29;SOR=1.179;VQSLOD=20.59;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,23:23:69:679,69,0 chr1 926250 rs2879816 G A 831.77 PASS AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=33.27;SOR=0.941;VQSLOD=22.26;culprit=QD GT:AD:DP:GQ:PL 1/1:0,25:25:75:860,75,0 chr1 926428 rs13302982 A G 625.77 PASS AC=2;AF=1.00;AN=2;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=28.44;SOR=0.874;VQSLOD=20.90;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,22:22:66:654,66,0 chr1 926713 rs13303291 T C 639.77 PASS AC=2;AF=1.00;AN=2;DB;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=30.47;SOR=1.508;VQSLOD=22.39;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,21:21:63:668,63,0 chr1 926744 rs13303101 A G 703.77 PASS AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=28.15;SOR=0.941;VQSLOD=22.10;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,25:25:74:732,74,0 chr1 927003 rs6680268 C T 715.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=25.71;SOR=1.061;VQSLOD=20.64;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,17:17:51:1|1:927003_C_T:744,51,0 chr1 927009 rs6693546 A G 680.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=32.40;SOR=1.244;VQSLOD=21.06;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,16:16:48:1|1:927003_C_T:709,48,0 chr1 927486 rs3892970 C T 834.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=32.11;SOR=1.220;VQSLOD=21.96;culprit=QD GT:AD:DP:GQ:PL 1/1:0,26:26:78:863,78,0 chr1 927744 rs4040604 G T 583.77 PASS AC=2;AF=1.00;AN=2;DB;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=32.43;SOR=0.914;VQSLOD=21.97;culprit=QD GT:AD:DP:GQ:PL 1/1:0,18:18:54:612,54,0 chr1 928131 rs28626846 T C 215.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.451e+00;ClippingRankSum=1.12;DB;DP=26;ExcessHet=3.0103;FS=6.186;MLEAC=1;MLEAF=0.500;MQ=57.67;MQRankSum=-1.177e+00;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=8.63;ReadPosRankSum=1.34;SOR=0.450;VQSLOD=-4.368e-01;culprit=MQ GT:AD:DP:GQ:PL 0/1:14,11:25:99:244,0,357 chr1 928176 rs7410998 G A 998.77 VQSRTrancheINDEL95.00to96.00;LowQual AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.74;POSITIVE_TRAIN_SITE;QD=32.52;SOR=1.179;VQSLOD=5.37;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,23:23:69:1|1:928176_G_A:1027,69,0 chr1 928182 rs7417972 A C 998.77 PASS AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.74;POSITIVE_TRAIN_SITE;QD=27.36;SOR=1.179;VQSLOD=5.60;culprit=QD GT:AD:DP:GQ:PGT:PID:PL 1/1:0,23:23:69:1|1:928176_G_A:1027,69,0 chr1 928309 rs7417994 A G 1123.77 PASS AC=2;AF=1.00;AN=2;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.58;POSITIVE_TRAIN_SITE;QD=29.57;SOR=0.798;VQSLOD=2.69;culprit=DP GT:AD:DP:GQ:PL 1/1:0,38:38:99:1152,114,0 chr1 929346 rs2340590 T A 916.77 PASS AC=2;AF=1.00;AN=2;DB;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=32.74;SOR=0.836;VQSLOD=21.64;culprit=QD GT:AD:DP:GQ:PL 1/1:0,28:28:84:945,84,0 chr1 929375 rs2340589 A G 1173.77 PASS AC=2;AF=1.00;AN=2;DB;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=29.05;SOR=0.922;VQSLOD=22.09;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,27:27:81:1|1:929375_A_G:1202,81,0 chr1 929377 rs2340588 G A 1173.77 PASS AC=2;AF=1.00;AN=2;DB;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=31.56;SOR=0.922;VQSLOD=22.17;culprit=MQ GT:AD:DP:GQ:PGT:PID:PL 1/1:0,27:27:81:1|1:929375_A_G:1202,81,0 chr1 929558 rs2340587 G A 1087.77 PASS AC=2;AF=1.00;AN=2;DB;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=31.08;SOR=1.002;VQSLOD=20.49;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,35:35:99:1116,105,0 chr2 929700 rs29938 G A,T 1087.77 VQSRTrancheINDEL95.00to96.00 AC=2;AF=1.00;AN=2;DB;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=31.08;SOR=1.002;VQSLOD=20.49;culprit=MQ GT:AD:DP:GQ:PL 1/2:0,35:35:99:1116,105,0 chr2 4312682 . C <NON_REF> . . END=4312686 GT:DP:GQ:MIN_DP:PL 0/0:34:90:32:0,90,1350 chr2 4312687 . G A,<NON_REF> 510.77 . BaseQRankSum=-0.547;ClippingRankSum=-0.426;DP=32;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.345;RAW_MQ=115200.00;ReadPosRankSum=-0.831 GT:AD:DP:GQ:PL:SB 0/1:12,19,0:31:99:539,0,324,576,381,957:5,7,9,10 chr2 4312688 . C <NON_REF> . . END=4312701 GT:DP:GQ:MIN_DP:PL 0/0:32:90:32:0,90,1350 chr2 4358121 . T <NON_REF> . . END=4358121 GT:DP:GQ:MIN_DP:PL 0/0:41:87:41:0,87,1291 chr2 4358122 . T <NON_REF> . . END=4358472 GT:DP:GQ:MIN_DP:PL 0/0:46:99:38:0,103,1277 chr2 4358473 . T C,<NON_REF> 773.77 . BaseQRankSum=-1.721;ClippingRankSum=0.407;DP=41;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.801;RAW_MQ=147600.00;ReadPosRankSum=0.775 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:18,23,0:41:99:0|1:4358473_T_C:802,0,958,856,1027,1883:12,6,8,15 chr2 4358474 . A <NON_REF> . . END=4358493 GT:DP:GQ:MIN_DP:PL 0/0:37:99:35:0,99,1218 chr2 4358494 . A <NON_REF> . . END=4358497 GT:DP:GQ:MIN_DP:PL 0/0:35:93:35:0,93,1395 chr2 4358498 . G A,<NON_REF> 651.77 . BaseQRankSum=-0.017;ClippingRankSum=0.466;DP=34;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.707;RAW_MQ=122400.00;ReadPosRankSum=0.707 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:16,18,0:34:99:0|1:4358473_T_C:680,0,907,728,961,1689:10,6,6,12 chr2 4358499 . T <NON_REF> . . END=4358499 GT:DP:GQ:MIN_DP:PL 0/0:35:79:35:0,79,1047 chr2 4358500 . G <NON_REF> . . END=4358504 GT:DP:GQ:MIN_DP:PL 0/0:37:90:36:0,90,1350 chr2 4358505 . C <NON_REF> . . END=4358505 GT:DP:GQ:MIN_DP:PL 0/0:40:99:40:0,99,1485 chr2 4358506 . A <NON_REF> . . END=4358506 GT:DP:GQ:MIN_DP:PL 0/0:39:86:39:0,86,1205 chr2 4358507 . T <NON_REF> . . END=4358508 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1485 chr2 4358509 . T <NON_REF> . . END=4358510 GT:DP:GQ:MIN_DP:PL 0/0:39:96:36:0,96,1440 chr2 4358511 . T <NON_REF> . . END=4358512 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 chr2 4358513 . T <NON_REF> . . END=4358513 GT:DP:GQ:MIN_DP:PL 0/0:36:96:36:0,96,1159 chr2 4358514 . T <NON_REF> . . END=4358514 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,105,1575 chr2 4358515 . C <NON_REF> . . END=4358515 GT:DP:GQ:MIN_DP:PL 0/0:37:96:37:0,96,1176 chr2 4358516 . A <NON_REF> . . END=4358523 GT:DP:GQ:MIN_DP:PL 0/0:37:99:37:0,99,1485 chr2 4358524 . G <NON_REF> . . END=4358524 GT:DP:GQ:MIN_DP:PL 0/0:37:95:37:0,95,1197 chr2 4358525 . T <NON_REF> . . END=4358526 GT:DP:GQ:MIN_DP:PL 0/0:37:99:36:0,99,1485 chr2 4358527 . A <NON_REF> . . END=4358542 GT:DP:GQ:MIN_DP:PL 0/0:33:90:33:0,90,1350 chr2 4358543 . T <NON_REF> . . END=4358549 GT:DP:GQ:MIN_DP:PL 0/0:33:84:31:0,84,1260 chr2 4358550 . A <NON_REF> . . END=4358555 GT:DP:GQ:MIN_DP:PL 0/0:34:90:33:0,90,1350 chr2 4358556 . T <NON_REF> . . END=4358556 GT:DP:GQ:MIN_DP:PL 0/0:34:99:34:0,99,1485 chr2 4358557 . C <NON_REF> . . END=4358557 GT:DP:GQ:MIN_DP:PL 0/0:34:87:34:0,87,1110 chr2 4358558 . T <NON_REF> . . END=4358668 GT:DP:GQ:MIN_DP:PL 0/0:41:99:34:0,99,1206 chr2 4358669 . G <NON_REF> . . END=4358669 GT:DP:GQ:MIN_DP:PL 0/0:39:99:39:0,99,1275 chr2 4358670 . T <NON_REF> . . END=4358695 GT:DP:GQ:MIN_DP:PL 0/0:41:99:39:0,106,1321 chr2 4358696 . C T,<NON_REF> 578.77 . BaseQRankSum=5.028;ClippingRankSum=-0.611;DP=44;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=1.527;RAW_MQ=158400.00;ReadPosRankSum=0.446 GT:AD:DP:GQ:PL:SB 0/1:23,21,0:44:99:607,0,513,675,577,1252:8,15,11,10 chr2 4358697 . G <NON_REF> 0 . END=4358702 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,99,1485 chr2 4358703 . A <NON_REF> 0 . END=4358716 GT:DP:GQ:MIN_DP:PL 0/0:35:90:30:0,90,1059 chr3 14319 . T TA,TAAA 649.73 PASS AC=1,1;AF=0.500,0.500;AN=2;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;QD=25.48;SOR=3.383;VQSLOD=3.40;culprit=FS GT:AD:DP:GQ:PL 1/2:0,10,7:17:99:687,256,250,387,0,346 chr3 50103 rs552943457 CT C,CTT 457.73 PASS AC=1,1;AF=0.500,0.500;AN=2;DB;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;QD=18.31;SOR=0.770;VQSLOD=3.64;culprit=FS GT:AD:DP:GQ:PL 1/2:0,16,9:25:99:495,194,213,362,0,444 chr3 116666 rs3079263 TAC T,TACAC 1277.73 PASS AC=1,1;AF=0.500,0.500;AN=2;DB;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;POSITIVE_TRAIN_SITE;QD=37.72;SOR=0.927;VQSLOD=7.70;culprit=QD GT:AD:DP:GQ:PL 1/2:0,21,15:36:99:1315,532,614,821,0,776 chr3 149380 rs2203258 T A,G 1047.77 PASS AC=1,1;AF=0.500,0.500;AN=2;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;POSITIVE_TRAIN_SITE;QD=27.57;SOR=0.798;VQSLOD=20.57;culprit=QD GT:AD:DP:GQ:PL 1/2:0,21,17:38:99:1076,494,431,583,0,532 chr3 241872 rs72352263 ATAAG A,GTAAG 1257.77 PASS AC=1,1;AF=0.500,0.500;AN=2;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;POSITIVE_TRAIN_SITE;QD=34.94;SOR=0.804;VQSLOD=7.04;culprit=FS GT:AD:DP:GQ:PL 1/2:0,21,15:36:99:1286,444,562,881,0,858 chr3 370537 rs142286746 C CA,CAA 350.73 PASS AC=1,1;AF=0.500,0.500;AN=2;DB;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;QD=26.98;SOR=1.179;VQSLOD=2.88;culprit=FS GT:AD:DP:GQ:PL 1/2:0,6,7:13:99:388,188,149,140,0,116 chrX 1052617 . C CAAAGGCTGCAATGTGAATGAATTTTTGGAAATAGCCCTAATGCTCATCTATGAAGGAGTGATAAACACAGCATCCTTTATCCATGCAATGGAATATTATGCAGTCTAGAAAAGGAATAAGGCTCTGACAAAAGACTGCAATATGTATGAATTTTGGAAACAGCCCTACTGCCCATCTATAAAGGAATGGATAAACACAGCATAGTTCATCTATACAATGCAATATTATAATGGAATATTATGCAGCCTGGAACAGGAACAAGGCTCTGAG 973.73 VQSRTrancheINDEL99.90to99.95 AC=1;AF=0.500;AN=2;BaseQRankSum=0.371;ClippingRankSum=0.454;DP=20;ExcessHet=3.0103;FS=2.017;MLEAC=1;MLEAF=0.500;MQ=59.81;MQRankSum=-1.443e+00;NEGATIVE_TRAIN_SITE;QD=32.39;ReadPosRankSum=-3.505e+00;SOR=1.219;VQSLOD=-2.143e+00;culprit=ReadPosRankSum GT:AD:DP:GQ:PGT:PID:PL 0/1:14,6:20:99:0|1:1052617_C_CAAAGGCTGCAATGTGAATGAATTTTTGGAAATAGCCCTAATGCTCATCTATGAAGGAGTGATAAACACAGCATCCTTTATCCATGCAATGGAATATTATGCAGTCTAGAAAAGGAATAAGGCTCTGACAAAAGACTGCAATATGTATGAATTTTGGAAACAGCCCTACTGCCCATCTATAAAGGAATGGATAAACACAGCATAGTTCATCTATACAATGCAATATTATAATGGAATATTATGCAGCCTGGAACAGGAACAAGGCTCTGAG:1011,0,154 chrX 1052888 . C T 973.73 VQSRTrancheINDEL99.90to99.95 AC=1;AF=0.500;AN=2;culprit=ReallyLongStringThatBreaksUint8xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxw GT:AD:DP:GQ:PGT:PID:PL 0/1:14,6:20:99:0|1:1052617_C_T:1011,0,154