VCF - D15780_S13_L001.vcf (小資料)

VCF - D15780_S13_L001.vcf (小資料) === ###### tags: `基因體/二級分析` ###### tags: `生物資訊`, `基因體`, `二級分析`, `VCF` [TOC] ## 目錄： - VCF 基本結構 - [D15780_S13_L001.vcf - header](#OUTPUT3HCD15780_S13_L001vcf---header) - [D15780_S13_L001.vcf - body - Sample](#OUTPUT3HCD15780_S13_L001vcf---body---Sample) - [D15780_S13_L001.vcf - body - all](#OUTPUT3HCD15780_S13_L001vcf---body---all) =================================== ![](https://us.v-cdn.net/5019796/uploads/FileUpload/70/9eec0b6faaa664f7630abddaf15594.png) ## OUTPUT/3.HC/D15780_S13_L001.vcf - header - 檔案格式＆版本 ##fileformat=**VCFv4.2** - 過濾器，用來過濾品質不好的序列如某個點有突變(SNP)，但可信度不高，就過濾掉 ##FILTER=<ID=**LowQual**,Description="**Low quality**"> - 產生此 VCF 檔的 GATK 指令 ##GATKCommandLine=<ID=**HaplotypeCaller**, CommandLine="**HaplotypeCaller** ... --dbsnp /Everythings/misc/bundle/b37/dbsnp_138.b37.vcf ...(more).. --output D15780_S13_L001.vcf ...(more).. --reference /Everythings/misc/bundle/b37/human_g1k_v37_decoy.fasta ...(more)", Version=4.1.0.0, Date="July 5, 2019 5:26:27 PM CST"> - 產生此 VCF 檔的來源工具 ##source=**HaplotypeCaller** - header 原始內容 ``` ##fileformat=VCFv4.2 檔案格式＆版本 ##FILTER=<ID=LowQual,Description="Low quality"> 過濾器，用來過濾品質不好的序列如某個點有突變(SNP)，但可信度不高，就過濾掉 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --dbsnp /Everythings/misc/bundle/b37/dbsnp_138.b37.vcf --pair-hmm-implementation AVX_LOGLESS_CACHING_OMP --native-pair-hmm-threads 2 --smith-waterman AVX_ENABLED --output D15780_S13_L001.vcf --intervals /Everythings/misc/bed/b37/Agilent_SureSelect_Human_All_Exon_V7_S31285117_Regions.b37.bed --input D15780_S13_L001.sorted.dedup.recal.bam --read-index D15780_S13_L001.sorted.dedup.recal.bam.bai --reference /Everythings/misc/bundle/b37/human_g1k_v37_decoy.fasta --tmp-dir . --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --adaptive-pruning false --do-not-recover-dangling-branches false --recover-dangling-heads false --consensus false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 1.0 --max-unpruned-variants 100 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --correct-overlapping-quality false --emit-ref-confidence NONE --use-new-qual-calculator true --use-old-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version=4.1.0.0,Date="July 5, 2019 5:26:27 PM CST"> 產生此 VCF 檔的 GATK 指令 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> ##INFO=<ID=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=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=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> ##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"> 底下是用 contig(片段重疊群) 來紀錄各個染色體，及其他序列的長度如人類的第1～22條是體染色體，第23條(X, Y)是性染色體 MT(mitochondrion) 粒線體染色體 GLXXXXXX 無法定位的因體片段序列 NC_007605 (NC:Nucleotide, 核苷酸) 人類疱疹病毒第四型體染色體的排序是根據序列，從長到短排序其中第21, 22條搞顛倒那是由於早年科學家的染色及辨識技術未臻成熟，致產生編排上的小誤差 ##contig=<ID=1,length=249250621> ##contig=<ID=2,length=243199373> ##contig=<ID=3,length=198022430> ##contig=<ID=4,length=191154276> ##contig=<ID=5,length=180915260> ##contig=<ID=6,length=171115067> ##contig=<ID=7,length=159138663> ##contig=<ID=8,length=146364022> ##contig=<ID=9,length=141213431> ##contig=<ID=10,length=135534747> ##contig=<ID=11,length=135006516> ##contig=<ID=12,length=133851895> ##contig=<ID=13,length=115169878> ##contig=<ID=14,length=107349540> ##contig=<ID=15,length=102531392> ##contig=<ID=16,length=90354753> ##contig=<ID=17,length=81195210> ##contig=<ID=18,length=78077248> ##contig=<ID=19,length=59128983> ##contig=<ID=20,length=63025520> ##contig=<ID=21,length=48129895> ##contig=<ID=22,length=51304566> ##contig=<ID=X,length=155270560> ##contig=<ID=Y,length=59373566> ##contig=<ID=MT,length=16569> GL000207.1 https://www.ncbi.nlm.nih.gov/nuccore/GL000207.1?report=genbank GL000226.1 https://www.ncbi.nlm.nih.gov/nuccore/224183275/ ##contig=<ID=GL000207.1,length=4262> ##contig=<ID=GL000226.1,length=15008> ##contig=<ID=GL000229.1,length=19913> ##contig=<ID=GL000231.1,length=27386> ##contig=<ID=GL000210.1,length=27682> ##contig=<ID=GL000239.1,length=33824> ##contig=<ID=GL000235.1,length=34474> ##contig=<ID=GL000201.1,length=36148> ##contig=<ID=GL000247.1,length=36422> ##contig=<ID=GL000245.1,length=36651> ##contig=<ID=GL000197.1,length=37175> ##contig=<ID=GL000203.1,length=37498> ##contig=<ID=GL000246.1,length=38154> ##contig=<ID=GL000249.1,length=38502> ##contig=<ID=GL000196.1,length=38914> ##contig=<ID=GL000248.1,length=39786> ##contig=<ID=GL000244.1,length=39929> ##contig=<ID=GL000238.1,length=39939> ##contig=<ID=GL000202.1,length=40103> ##contig=<ID=GL000234.1,length=40531> ##contig=<ID=GL000232.1,length=40652> ##contig=<ID=GL000206.1,length=41001> ##contig=<ID=GL000240.1,length=41933> ##contig=<ID=GL000236.1,length=41934> ##contig=<ID=GL000241.1,length=42152> ##contig=<ID=GL000243.1,length=43341> ##contig=<ID=GL000242.1,length=43523> ##contig=<ID=GL000230.1,length=43691> ##contig=<ID=GL000237.1,length=45867> ##contig=<ID=GL000233.1,length=45941> ##contig=<ID=GL000204.1,length=81310> ##contig=<ID=GL000198.1,length=90085> ##contig=<ID=GL000208.1,length=92689> ##contig=<ID=GL000191.1,length=106433> ##contig=<ID=GL000227.1,length=128374> ##contig=<ID=GL000228.1,length=129120> ##contig=<ID=GL000214.1,length=137718> ##contig=<ID=GL000221.1,length=155397> ##contig=<ID=GL000209.1,length=159169> ##contig=<ID=GL000218.1,length=161147> ##contig=<ID=GL000220.1,length=161802> ##contig=<ID=GL000213.1,length=164239> ##contig=<ID=GL000211.1,length=166566> ##contig=<ID=GL000199.1,length=169874> ##contig=<ID=GL000217.1,length=172149> ##contig=<ID=GL000216.1,length=172294> ##contig=<ID=GL000215.1,length=172545> ##contig=<ID=GL000205.1,length=174588> ##contig=<ID=GL000219.1,length=179198> ##contig=<ID=GL000224.1,length=179693> ##contig=<ID=GL000223.1,length=180455> ##contig=<ID=GL000195.1,length=182896> ##contig=<ID=GL000212.1,length=186858> ##contig=<ID=GL000222.1,length=186861> ##contig=<ID=GL000200.1,length=187035> ##contig=<ID=GL000193.1,length=189789> ##contig=<ID=GL000194.1,length=191469> ##contig=<ID=GL000225.1,length=211173> ##contig=<ID=GL000192.1,length=547496> ##contig=<ID=NC_007605,length=171823> ##contig=<ID=hs37d5,length=35477943> 產生此 VCF 檔的來源工具 ##source=HaplotypeCaller ``` <hr> ## OUTPUT/3.HC/D15780_S13_L001.vcf - body - Sample ``` #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT D15780_S13_L001 2 3749151 rs34308920 GGAA G 78.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=25.36;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 X 24381387 rs1207577 G C 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 X 24381409 rs142864280 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 ``` | 欄位 | Chrom-2 | Chrom-X1 | Chrom-X2 | | ------------------- | -------- | -------- | -------- | | **#CHROM** | 2 | X | X | | **POS** | 3749151 | 24381387 | 24381409 | | **ID** | rs34308920 | rs1207577 | rs142864280 | | **REF** | GGAA | G | G | | **ALT** | G | C | A | | **QUAL** | 78.28 | 37.28 | 37.28 | | **FILTER** | . | . | . | | **INFO** | AC=2; AF=1.00; AN=2; DB; DP=2; ExcessHet=3.0103; FS=0.000; MLEAC=1; MLEAF=0.500; MQ=60.00; QD=25.36; SOR=0.693 | AC=2; AF=1.00; AN=2; DB; DP=2; ExcessHet=3.0103; FS=0.000; MLEAC=1; MLEAF=0.500; MQ=60.00; QD=18.64; SOR=0.693 | AC=2; AF=1.00; AN=2; DB; DP=2; ExcessHet=3.0103; FS=0.000; MLEAC=1; MLEAF=0.500; MQ=60.00; QD=18.64; SOR=0.693 | | **FORMAT** | GT:AD:DP:GQ:PL | GT:AD:DP:GQ:PL | GT:AD:DP:GQ:PL | | **D15780_S13_L001** | 1/1:0,2:2:6:90,6,0 | 1/1:0,2:2:6:49,6,0 | 1/1:0,2:2:6:49,6,0 | - ### x1 (POS=24381387) - 屬性： ![](https://i.imgur.com/QRQzXT1.png) ![](https://i.imgur.com/5EiRl2i.png) - 最後兩個欄位 **FORMAT**：GT:AD:DP:GQ:PL **D15780_S13_L001**：1/1:0,2:2:6:49,6,0 - GT：1/1 (Genotype) - AD：0,2 (Allele Depth) - DP：2 (Read Depth) - GQ：6 (Genotype Quality) - PL：49,6,0 (Phred-scaled likelihoods) <hr> ## OUTPUT/3.HC/D15780_S13_L001.vcf - body - all ``` #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT D15780_S13_L001 1 69270 rs201219564 A G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=25.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1 2453163 rs78763061 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1 10190839 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1 11008206 rs186087187 C T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1 11087559 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1 11849447 rs868014 A G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1 16903912 rs61772344 T A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.03;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1 17413121 rs2076615 A C 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1 22191454 rs897471 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1 24134721 rs719400 T C 3296.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.718;DB;DP=124;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=26.58;ReadPosRankSum=-0.615;SOR=0.795 GT:AD:DP:GQ:PL 1/1:2,122:124:99:3310,322,0 1 45973928 rs2275276 G A 3365.03 . AC=2;AF=1.00;AN=2;DB;DP=125;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.14;SOR=0.828 GT:AD:DP:GQ:PL 1/1:0,124:124:99:3379,370,0 1 53675934 rs140853350 T C 32.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.967;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.87;ReadPosRankSum=0.967;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:30:40,0,30 1 100472604 rs534252 A G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1 146401761 . A T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1 153652292 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1 159505098 . T A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1 166135225 . GC G 59.28 . 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AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 5 178408795 rs373757775 C T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 6 26107944 rs12526092 C T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 6 29364787 rs3128853 C T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 6 30882634 rs1264302 C T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 6 30882781 rs1264301 G T 37.28 . 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AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 7 44281335 . C A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 7 148851273 rs3801979 G C 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 7 151483573 . T A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 7 151932908 rs112326730 T C 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 8 24211331 rs7814768 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 8 101153024 rs1460934 G A 36.28 . 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AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 9 32543635 . T C 67.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 9 32543643 . G A 67.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 9 80851350 rs10867166 G C 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 9 107620867 rs2230806 C T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 9 135263573 rs556386 G T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 10 26446312 rs3758449 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 10 97141523 rs2274490 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 10 99221876 . C A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 10 101373675 . T A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 10 124066764 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 11 608114 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 11 1887806 rs7938342 T A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 11 33373365 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 11 57982229 rs1966836 A G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 11 64577238 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 11 65732651 rs550435 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 11 107992346 rs3741056 G C 917.03 . AC=2;AF=1.00;AN=2;DB;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=26.20;SOR=0.869 GT:AD:DP:GQ:PL 1/1:0,35:35:99:931,104,0 11 124747427 . C T 37.28 . 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AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 12 51402905 rs445520 T G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 12 66605228 rs1152888 A G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 12 75715330 rs10879901 C A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 12 85466723 rs17012533 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 12 96387765 rs2302628 T A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 12 97102578 rs7968231 G A 35.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=17.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:47,6,0 12 103237468 rs772897 G C 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 12 109994870 rs9593 A T 595.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.108;DB;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=12.67;ReadPosRankSum=-0.850;SOR=0.586 GT:AD:DP:GQ:PL 0/1:20,27:47:99:603,0,456 12 110011229 rs10774774 G T 2225.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.785;DB;DP=174;ExcessHet=3.0103;FS=1.226;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=12.79;ReadPosRankSum=2.512;SOR=0.774 GT:AD:DP:GQ:PL 0/1:111,63:174:99:2233,0,5280 12 110011230 rs10774775 C T 2225.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DB;DP=173;ExcessHet=3.0103;FS=1.235;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=12.86;ReadPosRankSum=2.431;SOR=0.758 GT:AD:DP:GQ:PL 0/1:110,63:173:99:2233,0,5280 12 122261456 rs3741593 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 13 21371102 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 13 45147517 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 13 80911525 rs504122 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 14 24470690 . T TA 69.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=48.00;QD=34.66;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 14 24729844 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 14 44974966 rs1959379 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 14 44975052 rs3825630 A G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 14 44975606 rs3809429 G T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 14 73014061 rs61299139 T C 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 14 80164171 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 14 97321648 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 14 97321689 rs2230532 C T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 14 100834796 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 14 102457886 . T C 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 14 103059413 . G GC 52.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=26.16;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:64,6,0 14 103059447 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 14 105398669 . T A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 14 106090952 rs375494663 C T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 15 41105926 rs690347 T G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 15 41679717 rs73407109 C T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 15 85478410 rs2242048 A G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 16 424815 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 16 3169696 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 16 18823379 rs2606556 T C 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 16 20561190 rs7499739 G T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 16 57689385 rs1801257 C G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 16 68025801 rs255051 G C 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 16 77233394 rs4888607 A G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 16 88499539 rs9931465 C G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 16 89661807 rs12445560 C T 36.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.14;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:48,6,0 17 7121041 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 17 7400266 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 17 7453475 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 17 11833287 rs2286303 A G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 17 14095309 rs2230354 A G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 17 17925083 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 17 19564634 rs1800869 C G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 17 27580756 rs1047790 C T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 17 34100350 rs58543174 G GC 69.32 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=34.66;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 17 40120421 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 17 40364033 . C A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 17 48628470 rs9913430 T A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 17 63533087 rs145353986 C G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 17 63533602 . AGTG A 31.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.832;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=1.86;ReadPosRankSum=0.149;SOR=0.260 GT:AD:DP:GQ:PL 0/1:15,2:17:39:39,0,716 17 63533732 . ATGG A 31.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.960;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=1.86;ReadPosRankSum=-0.745;SOR=0.582 GT:AD:DP:GQ:PL 0/1:15,2:17:39:39,0,645 17 63533768 rs1133683 G A 248.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.391;DB;DP=16;ExcessHet=3.0103;FS=2.115;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=15.54;ReadPosRankSum=-2.999;SOR=0.636 GT:AD:DP:GQ:PL 0/1:9,7:16:99:256,0,534 17 63533789 rs9915936 T C 245.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.273;DB;DP=17;ExcessHet=3.0103;FS=4.560;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=14.45;ReadPosRankSum=-2.928;SOR=0.595 GT:AD:DP:GQ:PL 0/1:10,7:17:99:253,0,556 17 76503405 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 17 78935197 rs9899178 C T 35.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=17.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:47,6,0 17 78935233 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 18 2724930 rs633422 A T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 18 21119414 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 18 28666526 rs35717505 T TTAA 78.32 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=27.24;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 18 47803354 rs140686 C T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 18 48331553 rs2849233 T C 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 18 66504459 rs572020 A T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 18 77475486 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 830854 rs595844 T C 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 1063569 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 1528001 . C A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 2273037 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 5231419 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 8578000 rs1064010 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 15587202 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 39018728 rs908644 C G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 42930695 . C A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 48258717 rs1804994 A G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 48258772 rs11083895 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 50789859 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 51485622 rs2659067 A G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 54946764 . G T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 55668722 rs113899745 C CCTGT 78.32 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.20;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 19 55690373 rs201746906 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 19 56089543 . G A 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=25.00;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 19 56089549 rs199499964 G A 78.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.56;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 20 1285933 rs3795139 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 20 20177230 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 20 47253150 rs2664521 T C 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 20 48808269 . C T 32.61 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.87;ReadPosRankSum=-0.967;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:16:40,0,16 20 52601937 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 21 33719695 rs2070378 C T 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 21 38309459 rs61732502 C T 6786.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.248;DB;DP=714;ExcessHet=3.0103;FS=0.525;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=9.53;ReadPosRankSum=1.597;SOR=0.745 GT:AD:DP:GQ:PL 0/1:391,321:712:99:6794,0,9281 21 38309619 rs61732504 C A 3871.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.832;DB;DP=404;ExcessHet=3.0103;FS=0.581;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=9.63;ReadPosRankSum=0.842;SOR=0.759 GT:AD:DP:GQ:PL 0/1:227,175:402:99:3879,0,5949 21 38525603 rs7284020 A G 36.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.14;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:48,6,0 21 42613839 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 22 23114327 rs6003299 T C 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 22 23114350 rs5996382 A G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 22 23247082 rs2009433 C G 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 22 23247095 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 X 24381387 rs1207577 G C 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 X 24381409 rs142864280 G A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 X 104463840 . C T 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 X 135474420 rs1329546 C A 37.28 . AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 ```