KeepLearningBigData

基因数据处理34之使用samtools和bcftools进行变异分析

1.指令：
（1）

samtools mpileup -vf Homo_sapiens_assembly19chr20.fasta NA12878_snp_A2G_chr20_225058.sorted.bam > NA12878_snp_A2G_chr20_225058.variants

或者：

samtools mpileup -vf Homo_sapiens_assembly19chr20.fasta NA12878_snp_A2G_chr20_225058.sorted.bam > NA12878_snp_A2G_chr20_225058.vcf

（2）

bcftools call -mv NA12878_snp_A2G_chr20_225058.vcf >NA12878_snp_A2G_chr20_225058.raw.vcf

（3）

bcftools filter -s LowQual -e '%QUAL<20 || DP>100' NA12878_snp_A2G_chr20_225058.raw.vcf  > NA12878_snp_A2G_chr20_225058.flt.vcf

bcftools view 可以查看bcf数据结果。

结果：

xubo@xubo:~/xubo/data/avocado/NA12878_snp_A2G_chr20$ cat NA12878_snp_A2G_chr20_225058.flt.vcf 
##fileformat=VCFv4.2
##FILTER=
##samtoolsVersion=1.3.1-24-gf458b7c+htslib-1.3.1-35-g481752c
##samtoolsCommand=samtools mpileup -vf Homo_sapiens_assembly19chr20.fasta NA12878_snp_A2G_chr20_225058.sorted.bam
##reference=file://Homo_sapiens_assembly19chr20.fasta
##contig=
##ALT=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##FORMAT=
##FORMAT=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##bcftools_callVersion=1.3.1-15-g7c7c7a2+htslib-1.3.1-35-g481752c
##bcftools_callCommand=call -mv NA12878_snp_A2G_chr20_225058.vcf
##FILTER=100">
##bcftools_filterVersion=1.3.1-15-g7c7c7a2+htslib-1.3.1-35-g481752c
##bcftools_filterCommand=filter -s LowQual -e '%QUAL<20 || DP>100' NA12878_snp_A2G_chr20_225058.raw.vcf
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NA12878
20  224971  .   G   A   57  PASS    DP=8;VDB=0.0132829;SGB=-0.556411;RPB=0.405132;MQB=1.01283;MQSB=1.01283;BQB=0.810265;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=3,0,0,4;MQ=60  GT:PL 0/1:90,0,70
20  225058  .   A   G   217 PASS    DP=81;VDB=0.824099;SGB=-0.693139;RPB=0.952244;MQB=0.978845;MQSB=0.987634;BQB=3.33479e-07;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=25,14,21,15;MQ=59   GT:PL   0/1:250,0,255

与Avocado结果一致

参考：
【1】 http://www.htslib.org/doc/samtools.html

附录中间结果：

xubo@xubo:~/xubo/data/avocado/NA12878_snp_A2G_chr20$ bcftools view NA12878_snp_A2G_chr20_225058.variants 
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##samtoolsVersion=1.3.1-24-gf458b7c+htslib-1.3.1-35-g481752c
##samtoolsCommand=samtools mpileup -vf Homo_sapiens_assembly19chr20.fasta NA12878_snp_A2G_chr20_225058.sorted.bam
##reference=file://Homo_sapiens_assembly19chr20.fasta
##contig=<ID=20,length=63025520>
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##bcftools_viewVersion=1.3.1-15-g7c7c7a2+htslib-1.3.1-35-g481752c
##bcftools_viewCommand=view NA12878_snp_A2G_chr20_225058.variants
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NA12878
20  224959  .   C   <*> 0   .   DP=1;I16=0,1,0,0,27,729,0,0,60,3600,0,0,0,0,0,0;QS=1,0;MQ0F=0   PL  0,3,27
20  224960  .   A   <*> 0   .   DP=1;I16=0,1,0,0,33,1089,0,0,60,3600,0,0,1,1,0,0;QS=1,0;MQ0F=0  PL  0,3,33
20  224961  .   T   <*> 0   .   DP=2;I16=0,2,0,0,54,1586,0,0,120,7200,0,0,2,4,0,0;QS=1,0;MQ0F=0 PL  0,6,50
20  224962  .   C   <*> 0   .   DP=4;I16=1,3,0,0,127,4041,0,0,240,14400,0,0,4,10,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,12,112
20  224963  .   A   <*> 0   .   DP=4;I16=1,3,0,0,132,4358,0,0,240,14400,0,0,8,22,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,12,115
20  224964  .   G   <*> 0   .   DP=4;I16=1,3,0,0,132,4370,0,0,240,14400,0,0,12,42,0,0;QS=1,0;MQSB=1;MQ0F=0  PL  0,12,115
20  224965  .   A   <*> 0   .   DP=5;I16=2,3,0,0,169,5737,0,0,300,18000,0,0,16,70,0,0;QS=1,0;MQSB=1;MQ0F=0  PL  0,15,148
20  224966  .   A   <*> 0   .   DP=5;I16=2,3,0,0,159,5191,0,0,300,18000,0,0,21,107,0,0;QS=1,0;MQSB=1;MQ0F=0 PL  0,15,139
20  224967  .   A   <*> 0   .   DP=6;I16=2,4,0,0,195,6415,0,0,360,21600,0,0,26,154,0,0;QS=1,0;MQSB=1;MQ0F=0 PL  0,18,160
20  224968  .   A   <*> 0   .   DP=7;I16=3,4,0,0,231,7707,0,0,420,25200,0,0,32,212,0,0;QS=1,0;MQSB=1.01283;MQ0F=0   PL  0,21,184
20  224969  .   C   <*> 0   .   DP=7;I16=3,4,0,0,236,7980,0,0,420,25200,0,0,39,283,0,0;QS=1,0;MQSB=1.01283;MQ0F=0   PL  0,21,188
20  224970  .   T   <*> 0   .   DP=8;I16=3,4,0,0,245,8593,0,0,420,25200,0,0,46,368,0,0;QS=1,0;MQSB=1.01283;MQ0F=0   PL  0,21,195
20  224971  .   G   A,<*>   0   .   DP=8;I16=3,0,0,4,106,3746,139,4851,180,10800,240,14400,18,126,35,341;QS=0.432653,0.567347,0;VDB=0.0132829;SGB=-0.556411;RPB=0.405132;MQB=1.01283;MQSB=1.01283;BQB=0.810265;MQ0F=0   PL  90,0,70,99,82,166
20  224972  .   A   <*> 0   .   DP=8;I16=3,4,0,0,256,9364,0,0,420,25200,0,0,60,580,0,0;QS=1,0;MQSB=1.01283;MQ0F=0   PL  0,21,202
20  224973  .   G   <*> 0   .   DP=9;I16=4,5,0,0,303,10283,0,0,540,32400,0,0,70,716,0,0;QS=1,0;MQSB=0.974597;MQ0F=0 PL  0,27,222
20  224974  .   A   <*> 0   .   DP=10;I16=5,5,0,0,347,12087,0,0,600,36000,0,0,79,865,0,0;QS=1,0;MQSB=0.952347;MQ0F=0    PL  0,30,245
20  224975  .   A   <*> 0   .   DP=10;I16=5,5,0,0,345,12037,0,0,600,36000,0,0,89,1033,0,0;QS=1,0;MQSB=0.952347;MQ0F=0   PL  0,30,245
20  224976  .   T   <*> 0   .   DP=11;I16=6,5,0,0,376,13014,0,0,660,39600,0,0,99,1221,0,0;QS=1,0;MQSB=0.950952;MQ0F=0   PL  0,33,255
20  224977  .   C   <*> 0   .   DP=12;I16=7,5,0,0,405,13713,0,0,720,43200,0,0,110,1430,0,0;QS=1,0;MQSB=0.95494;MQ0F=0   PL  0,36,255
20  224978  .   A   <*> 0   .   DP=12;I16=7,5,0,0,425,15099,0,0,720,43200,0,0,122,1662,0,0;QS=1,0;MQSB=0.95494;MQ0F=0   PL  0,36,255
20  224979  .   A   <*> 0   .   DP=12;I16=7,5,0,0,439,16071,0,0,720,43200,0,0,134,1918,0,0;QS=1,0;MQSB=0.95494;MQ0F=0   PL  0,36,255
20  224980  .   G   <*> 0   .   DP=15;I16=8,7,0,0,502,17056,0,0,900,54000,0,0,146,2198,0,0;QS=1,0;MQSB=1;MQ0F=0 PL  0,45,255
20  224981  .   G   <*> 0   .   DP=16;I16=9,7,0,0,542,18466,0,0,960,57600,0,0,161,2505,0,0;QS=1,0;MQSB=1;MQ0F=0 PL  0,48,255
20  224982  .   A   <*> 0   .   DP=16;I16=9,7,0,0,557,19493,0,0,960,57600,0,0,177,2843,0,0;QS=1,0;MQSB=1;MQ0F=0 PL  0,48,255
20  224983  .   T   <*> 0   .   DP=16;I16=9,7,0,0,545,18627,0,0,960,57600,0,0,193,3213,0,0;QS=1,0;MQSB=1;MQ0F=0 PL  0,48,255
20  224984  .   A   <*> 0   .   DP=17;I16=10,7,0,0,596,20950,0,0,1020,61200,0,0,209,3615,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,51,255
20  224985  .   G   <*> 0   .   DP=17;I16=10,7,0,0,582,20016,0,0,1020,61200,0,0,225,3999,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,51,255
20  224986  .   A   <*> 0   .   DP=19;I16=12,7,0,0,657,22891,0,0,1140,68400,0,0,241,4415,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,57,255
20  224987  .   A   <*> 0   .   DP=19;I16=12,6,0,0,634,22430,0,0,1080,64800,0,0,251,4765,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,54,255
20  224988  .   T   <*> 0   .   DP=21;I16=13,8,0,0,716,24646,0,0,1260,75600,0,0,273,5145,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,63,255
20  224989  .   T   <*> 0   .   DP=21;I16=13,8,0,0,728,25366,0,0,1260,75600,0,0,290,5508,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,63,255
20  224990  .   T   <*> 0   .   DP=23;I16=15,8,0,0,793,27491,0,0,1380,82800,0,0,307,5905,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,69,255
20  224991  .   C   <*> 0   .   DP=23;I16=15,8,0,0,792,27322,0,0,1380,82800,0,0,325,6287,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,69,255
20  224992  .   T   <*> 0   .   DP=23;I16=15,8,0,0,811,28691,0,0,1380,82800,0,0,343,6705,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,69,255
20  224993  .   A   <*> 0   .   DP=25;I16=15,9,0,0,858,30696,0,0,1440,86400,0,0,360,7108,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,72,255
20  224994  .   G   <*> 0   .   DP=27;I16=17,10,0,0,931,32225,0,0,1620,97200,0,0,388,7616,0,0;QS=1,0;MQSB=1;MQ0F=0  PL  0,81,255
20  224995  .   A   <*> 0   .   DP=28;I16=18,10,0,0,975,34429,0,0,1680,100800,0,0,408,8062,0,0;QS=1,0;MQSB=1;MQ0F=0 PL  0,84,255
20  224996  .   A   <*> 0   .   DP=29;I16=18,11,0,0,1010,35616,0,0,1740,104400,0,0,428,8498,0,0;QS=1,0;MQSB=1;MQ0F=0    PL  0,87,255
20  224997  .   A   <*> 0   .   DP=29;I16=18,11,0,0,1036,37180,0,0,1740,104400,0,0,449,8975,0,0;QS=1,0;MQSB=1;MQ0F=0    PL  0,87,255
20  224998  .   G   <*> 0   .   DP=30;I16=19,11,0,0,1007,34239,0,0,1800,108000,0,0,470,9494,0,0;QS=1,0;MQSB=1;MQ0F=0    PL  0,90,255
20  224999  .   T   <*> 0   .   DP=31;I16=20,11,0,0,1044,35740,0,0,1860,111600,0,0,491,10005,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,93,255
20  225000  .   T   <*> 0   .   DP=33;I16=22,10,0,0,1105,38627,0,0,1920,115200,0,0,495,10219,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,96,255
20  225001  .   C   <*> 0   .   DP=35;I16=24,10,0,0,1144,39032,0,0,2040,122400,0,0,517,10731,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,102,255
20  225002  .   C   <*> 0   .   DP=35;I16=24,10,0,0,1179,41045,0,0,2040,122400,0,0,540,11238,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,102,255
20  225003  .   T   <*> 0   .   DP=35;I16=24,11,0,0,1240,44402,0,0,2100,126000,0,0,582,12140,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,105,255
20  225004  .   T   <*> 0   .   DP=37;I16=25,11,0,0,1238,43018,0,0,2160,129600,0,0,584,12286,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,108,255
20  225005  .   C   <*> 0   .   DP=37;I16=25,12,0,0,1273,44191,0,0,2220,133200,0,0,630,13362,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,111,255
20  225006  .   C   <*> 0   .   DP=37;I16=25,12,0,0,1281,44737,0,0,2220,133200,0,0,652,13894,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,111,255
20  225007  .   C   <*> 0   .   DP=37;I16=25,12,0,0,1305,46243,0,0,2220,133200,0,0,673,14419,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,111,255
20  225008  .   C   <*> 0   .   DP=39;I16=26,13,0,0,1347,46837,0,0,2340,140400,0,0,694,14986,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,117,255
20  225009  .   T   <*> 0   .   DP=39;I16=26,13,0,0,1382,49302,0,0,2340,140400,0,0,716,15546,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,117,255
20  225010  .   A   <*> 0   .   DP=39;I16=26,13,0,0,1375,48677,0,0,2340,140400,0,0,737,16099,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,117,255
20  225011  .   A   <*> 0   .   DP=39;I16=25,13,0,0,1382,50392,0,0,2280,136800,0,0,733,16069,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,114,255
20  225012  .   A   <*> 0   .   DP=39;I16=26,12,0,0,1379,50223,0,0,2280,136800,0,0,752,16604,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,114,255
20  225013  .   G   <*> 0   .   DP=39;I16=26,12,0,0,1334,46938,0,0,2280,136800,0,0,771,17177,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,114,255
20  225014  .   C   <*> 0   .   DP=39;I16=26,13,0,0,1353,47331,0,0,2340,140400,0,0,813,18311,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,117,255
20  225015  .   T   <*> 0   .   DP=40;I16=27,13,0,0,1417,50887,0,0,2400,144000,0,0,830,18854,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,120,255
20  225016  .   T   <*> 0   .   DP=40;I16=27,13,0,0,1413,50181,0,0,2400,144000,0,0,846,19330,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,120,255
20  225017  .   T   <*> 0   .   DP=40;I16=27,12,0,0,1379,49151,0,0,2340,140400,0,0,837,19213,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,117,255
20  225018  .   C   <*> 0   .   DP=41;I16=28,13,0,0,1417,49427,0,0,2460,147600,0,0,878,20378,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,123,255
20  225019  .   A   <*> 0   .   DP=44;I16=30,13,0,0,1489,52043,0,0,2580,154800,0,0,894,20900,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,129,255
20  225020  .   C   <*> 0   .   DP=46;I16=31,15,0,0,1528,51118,0,0,2760,165600,0,0,921,21475,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,138,255
20  225021  .   A   <*> 0   .   DP=48;I16=32,15,0,0,1588,54544,0,0,2820,169200,0,0,939,21935,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,141,255
20  225022  .   C   <*> 0   .   DP=48;I16=32,16,0,0,1589,53249,0,0,2880,172800,0,0,967,22481,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,144,255
20  225023  .   T   <*> 0   .   DP=49;I16=32,17,0,0,1731,61681,0,0,2940,176400,0,0,986,22984,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,148,255
20  225024  .   T   <*> 0   .   DP=49;I16=32,17,0,0,1684,58626,0,0,2940,176400,0,0,1005,23475,0,0;QS=1,0;MQSB=1;MQ0F=0  PL  0,148,255
20  225025  .   G   <*> 0   .   DP=52;I16=34,18,0,0,1744,59236,0,0,3120,187200,0,0,1023,23953,0,0;QS=1,0;MQSB=1;MQ0F=0  PL  0,157,255
20  225026  .   C   <*> 0   .   DP=53;I16=35,17,0,0,1781,61425,0,0,3120,187200,0,0,1025,24079,0,0;QS=1,0;MQSB=1;MQ0F=0  PL  0,157,255
20  225027  .   C   <*> 0   .   DP=54;I16=36,18,0,0,1847,63779,0,0,3240,194400,0,0,1060,24720,0,0;QS=1,0;MQSB=1;MQ0F=0  PL  0,163,255
20  225028  .   T   <*> 0   .   DP=55;I16=37,18,0,0,1929,68767,0,0,3269,195241,0,0,1079,25109,0,0;QS=1,0;MQSB=0.987054;MQ0F=0   PL  0,166,255
20  225029  .   C   <*> 0   .   DP=55;I16=37,18,0,0,1884,65034,0,0,3269,195241,0,0,1099,25537,0,0;QS=1,0;MQSB=0.987054;MQ0F=0   PL  0,166,255
20  225030  .   A   <*> 0   .   DP=58;I16=39,19,0,0,2019,70909,0,0,3449,206041,0,0,1117,25903,0,0;QS=1,0;MQSB=0.98769;MQ0F=0    PL  0,175,255
20  225031  .   G   <*> 0   .   DP=58;I16=39,18,0,0,1951,67385,0,0,3389,202441,0,0,1116,25824,0,0;QS=1,0;MQSB=0.988135;MQ0F=0   PL  0,172,255
20  225032  .   T   <*> 0   .   DP=59;I16=40,18,0,0,1975,67771,0,0,3449,206041,0,0,1136,26226,0,0;QS=1,0;MQSB=0.988625;MQ0F=0   PL  0,175,255
20  225033  .   G   <*> 0   .   DP=59;I16=40,18,0,0,1957,66637,0,0,3449,206041,0,0,1157,26669,0,0;QS=1,0;MQSB=0.988625;MQ0F=0   PL  0,175,255
20  225034  .   T   <*> 0   .   DP=61;I16=41,19,0,0,2045,70271,0,0,3569,213241,0,0,1201,27677,0,0;QS=1,0;MQSB=0.988669;MQ0F=0   PL  0,181,255
20  225035  .   A   <*> 0   .   DP=61;I16=41,20,0,0,2108,73564,0,0,3629,216841,0,0,1245,28675,0,0;QS=1,0;MQSB=0.988268;MQ0F=0   PL  0,184,255
20  225036  .   T   <*> 0   .   DP=61;I16=41,20,0,0,2118,74190,0,0,3629,216841,0,0,1264,29090,0,0;QS=1,0;MQSB=0.988268;MQ0F=0   PL  0,184,255
20  225037  .   A   <*> 0   .   DP=61;I16=41,19,0,0,2095,73559,0,0,3569,213241,0,0,1257,28873,0,0;QS=1,0;MQSB=0.988669;MQ0F=0   PL  0,181,255
20  225038  .   T   <*> 0   .   DP=61;I16=41,20,0,0,2080,71942,0,0,3629,216841,0,0,1297,29801,0,0;QS=1,0;MQSB=0.988268;MQ0F=0   PL  0,184,255
20  225039  .   A   <*> 0   .   DP=62;I16=42,20,0,0,2117,73267,0,0,3689,220441,0,0,1312,30150,0,0;QS=1,0;MQSB=0.988726;MQ0F=0   PL  0,187,255
20  225040  .   T   <*> 0   .   DP=62;I16=42,19,0,0,2133,75291,0,0,3629,216841,0,0,1303,29921,0,0;QS=1,0;MQSB=0.989115;MQ0F=0   PL  0,184,255
20  225041  .   G   <*> 0   .   DP=63;I16=42,20,0,0,2049,69025,0,0,3689,220441,0,0,1342,30890,0,0;QS=1,0;MQSB=0.988726;MQ0F=0   PL  0,187,255
20  225042  .   T   A,<*>   0   .   DP=64;I16=42,20,1,0,2062,70408,28,784,3689,220441,60,3600,1314,30096,25,625;QS=0.98659,0.01341,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=0.989158;BQB=1;MQ0F=0   PL  0,161,255,187,255,255
20  225043  .   G   <*> 0   .   DP=64;I16=42,21,0,0,2144,73654,0,0,3749,224041,0,0,1354,31130,0,0;QS=1,0;MQSB=0.98835;MQ0F=0    PL  0,190,255
20  225044  .   G   <*> 0   .   DP=66;I16=43,22,0,0,2171,74097,0,0,3869,231241,0,0,1367,31493,0,0;QS=1,0;MQSB=0.988439;MQ0F=0   PL  0,196,255
20  225045  .   C   <*> 0   .   DP=68;I16=45,23,0,0,2260,76838,0,0,4049,242041,0,0,1405,32435,0,0;QS=1,0;MQSB=0.98895;MQ0F=0    PL  0,205,255
20  225046  .   T   <*> 0   .   DP=68;I16=45,23,0,0,2319,81177,0,0,4049,242041,0,0,1417,32657,0,0;QS=1,0;MQSB=0.98895;MQ0F=0    PL  0,205,255
20  225047  .   A   <*> 0   .   DP=68;I16=45,23,0,0,2256,76866,0,0,4049,242041,0,0,1428,32884,0,0;QS=1,0;MQSB=0.98895;MQ0F=0    PL  0,205,255
20  225048  .   T   <*> 0   .   DP=68;I16=45,22,0,0,2228,75892,0,0,3989,238441,0,0,1414,32540,0,0;QS=1,0;MQSB=0.989274;MQ0F=0   PL  0,202,255
20  225049  .   A   <*> 0   .   DP=70;I16=46,20,0,0,2149,71849,0,0,3929,234841,0,0,1389,32189,0,0;QS=1,0;MQSB=0.990313;MQ0F=0   PL  0,199,255
20  225050  .   C   <*> 0   .   DP=70;I16=46,23,0,0,2229,73289,0,0,4109,245641,0,0,1457,33641,0,0;QS=1,0;MQSB=0.989343;MQ0F=0   PL  0,208,255
20  225051  .   C   <*> 0   .   DP=70;I16=45,24,0,0,2290,77206,0,0,4140,248400,0,0,1465,33883,0,0;QS=1,0;MQSB=1;MQ0F=0  PL  0,208,255
20  225052  .   A   <*> 0   .   DP=70;I16=45,23,0,0,2259,76893,0,0,4049,242041,0,0,1443,33309,0,0;QS=1,0;MQSB=0.98895;MQ0F=0    PL  0,205,255
20  225053  .   C   <*> 0   .   DP=71;I16=46,25,0,0,2298,75208,0,0,4229,252841,0,0,1494,34560,0,0;QS=1,0;MQSB=0.988741;MQ0F=0   PL  0,214,255
20  225054  .   T   <*> 0   .   DP=71;I16=46,25,0,0,2410,83520,0,0,4229,252841,0,0,1496,34612,0,0;QS=1,0;MQSB=0.988741;MQ0F=0   PL  0,214,255
20  225055  .   G   <*> 0   .   DP=71;I16=45,25,0,0,2336,78822,0,0,4169,249241,0,0,1475,34187,0,0;QS=1,0;MQSB=0.988331;MQ0F=0   PL  0,211,255
20  225056  .   A   <*> 0   .   DP=73;I16=46,24,0,0,2359,80979,0,0,4169,249241,0,0,1472,34088,0,0;QS=1,0;MQSB=0.989038;MQ0F=0   PL  0,211,255
20  225057  .   C   <*> 0   .   DP=77;I16=46,25,0,0,2183,68947,0,0,4229,252841,0,0,1510,35040,0,0;QS=1,0;MQSB=0.988741;MQ0F=0   PL  0,214,255
20  225058  .   A   G,<*>   0   .   DP=81;I16=25,14,21,15,1348,46912,1002,28878,2340,140400,2129,126841,832,19188,766,17860;QS=0.573617,0.426383,0;VDB=0.824099;SGB=-0.693139;RPB=0.952244;MQB=0.978845;MQSB=0.987634;BQB=3.33479e-07;MQ0F=0    PL  250,0,255,255,255,255
20  225059  .   G   <*> 0   .   DP=81;I16=46,32,0,0,2618,88958,0,0,4649,278041,0,0,1639,37793,0,0;QS=1,0;MQSB=0.986878;MQ0F=0   PL  0,235,255
20  225060  .   G   <*> 0   .   DP=80;I16=46,31,0,0,2500,83826,0,0,4589,274441,0,0,1626,37590,0,0;QS=1,0;MQSB=0.987124;MQ0F=0   PL  0,232,255
20  225061  .   C   <*> 0   .   DP=80;I16=47,32,0,0,2634,89812,0,0,4709,281641,0,0,1630,37550,0,0;QS=1,0;MQSB=0.987315;MQ0F=0   PL  0,238,255
20  225062  .   C   <*> 0   .   DP=79;I16=47,31,0,0,2470,79782,0,0,4649,278041,0,0,1624,37416,0,0;QS=1,0;MQSB=0.987555;MQ0F=0   PL  0,235,255
20  225063  .   G   <*> 0   .   DP=77;I16=46,30,0,0,2280,69662,0,0,4529,270841,0,0,1620,37340,0,0;QS=1,0;MQSB=0.987376;MQ0F=0   PL  0,229,255
20  225064  .   C   <*> 0   .   DP=77;I16=45,30,0,0,2616,91594,0,0,4469,267241,0,0,1592,36738,0,0;QS=1,0;MQSB=0.986928;MQ0F=0   PL  0,226,255
20  225065  .   C   <*> 0   .   DP=76;I16=45,30,0,0,2654,94076,0,0,4469,267241,0,0,1586,36672,0,0;QS=1,0;MQSB=0.986928;MQ0F=0   PL  0,226,255
20  225066  .   A   <*> 0   .   DP=75;I16=43,30,0,0,2614,94244,0,0,4349,260041,0,0,1569,36463,0,0;QS=1,0;MQSB=0.985958;MQ0F=0   PL  0,220,255
20  225067  .   G   <*> 0   .   DP=74;I16=43,30,0,0,2506,86398,0,0,4349,260041,0,0,1563,36431,0,0;QS=1,0;MQSB=0.985958;MQ0F=0   PL  0,220,255
20  225068  .   T   <*> 0   .   DP=73;I16=43,29,0,0,2514,88542,0,0,4289,256441,0,0,1556,36352,0,0;QS=1,0;MQSB=0.986238;MQ0F=0   PL  0,217,255
20  225069  .   C   <*> 0   .   DP=72;I16=42,29,0,0,2473,86619,0,0,4229,252841,0,0,1549,36273,0,0;QS=1,0;MQSB=0.985718;MQ0F=0   PL  0,214,255
20  225070  .   A   <*> 0   .   DP=72;I16=42,29,0,0,2528,90620,0,0,4229,252841,0,0,1538,36044,0,0;QS=1,0;MQSB=0.985718;MQ0F=0   PL  0,214,255
20  225071  .   T   <*> 0   .   DP=71;I16=42,28,0,0,2499,89623,0,0,4169,249241,0,0,1525,35713,0,0;QS=1,0;MQSB=0.986014;MQ0F=0   PL  0,211,255
20  225072  .   T   <*> 0   .   DP=71;I16=42,28,0,0,2499,89435,0,0,4169,249241,0,0,1511,35379,0,0;QS=1,0;MQSB=0.986014;MQ0F=0   PL  0,211,255
20  225073  .   A   <*> 0   .   DP=71;I16=42,28,0,0,2463,87069,0,0,4169,249241,0,0,1497,35093,0,0;QS=1,0;MQSB=0.986014;MQ0F=0   PL  0,211,255
20  225074  .   A   <*> 0   .   DP=70;I16=41,28,0,0,2457,88171,0,0,4109,245641,0,0,1481,34705,0,0;QS=1,0;MQSB=0.985472;MQ0F=0   PL  0,208,255
20  225075  .   A   <*> 0   .   DP=69;I16=40,28,0,0,2449,88339,0,0,4049,242041,0,0,1463,34213,0,0;QS=1,0;MQSB=0.984898;MQ0F=0   PL  0,205,255
20  225076  .   T   <*> 0   .   DP=69;I16=40,28,0,0,2438,87596,0,0,4049,242041,0,0,1443,33667,0,0;QS=1,0;MQSB=0.984898;MQ0F=0   PL  0,205,255
20  225077  .   T   <*> 0   .   DP=69;I16=40,28,0,0,2439,87765,0,0,4049,242041,0,0,1421,33071,0,0;QS=1,0;MQSB=0.984898;MQ0F=0   PL  0,205,255
20  225078  .   C   <*> 0   .   DP=68;I16=39,28,0,0,2329,81449,0,0,3989,238441,0,0,1400,32526,0,0;QS=1,0;MQSB=0.984288;MQ0F=0   PL  0,202,255
20  225079  .   A   <*> 0   .   DP=68;I16=39,29,0,0,2399,84889,0,0,4049,242041,0,0,1389,32101,0,0;QS=1,0;MQSB=0.983965;MQ0F=0   PL  0,205,255
20  225080  .   A   <*> 0   .   DP=68;I16=39,29,0,0,2409,86149,0,0,4049,242041,0,0,1363,31435,0,0;QS=1,0;MQSB=0.983965;MQ0F=0   PL  0,205,255
20  225081  .   G   <*> 0   .   DP=65;I16=38,27,0,0,2258,78780,0,0,3869,231241,0,0,1340,30822,0,0;QS=1,0;MQSB=0.983981;MQ0F=0   PL  0,196,255
20  225082  .   C   <*> 0   .   DP=64;I16=37,27,0,0,2204,76498,0,0,3809,227641,0,0,1318,30258,0,0;QS=1,0;MQSB=0.983301;MQ0F=0   PL  0,193,255
20  225083  .   T   <*> 0   .   DP=64;I16=37,27,0,0,2301,82983,0,0,3809,227641,0,0,1296,29742,0,0;QS=1,0;MQSB=0.983301;MQ0F=0   PL  0,193,255
20  225084  .   C   <*> 0   .   DP=63;I16=37,26,0,0,2163,74877,0,0,3749,224041,0,0,1272,29124,0,0;QS=1,0;MQSB=0.983665;MQ0F=0   PL  0,190,255
20  225085  .   C   <*> 0   .   DP=62;I16=36,26,0,0,2107,72679,0,0,3689,220441,0,0,1247,28455,0,0;QS=1,0;MQSB=0.982951;MQ0F=0   PL  0,187,255
20  225086  .   A   <*> 0   .   DP=62;I16=36,26,0,0,2166,76070,0,0,3689,220441,0,0,1222,27836,0,0;QS=1,0;MQSB=0.982951;MQ0F=0   PL  0,187,255
20  225087  .   A   <*> 0   .   DP=61;I16=35,26,0,0,2195,79377,0,0,3629,216841,0,0,1197,27217,0,0;QS=1,0;MQSB=0.982188;MQ0F=0   PL  0,184,255
20  225088  .   G   <*> 0   .   DP=61;I16=35,26,0,0,2092,72304,0,0,3629,216841,0,0,1171,26599,0,0;QS=1,0;MQSB=0.982188;MQ0F=0   PL  0,184,255
20  225089  .   A   <*> 0   .   DP=59;I16=33,25,0,0,2054,73404,0,0,3480,208800,0,0,1122,25406,0,0;QS=1,0;MQSB=1;MQ0F=0  PL  0,175,255
20  225090  .   G   <*> 0   .   DP=59;I16=34,25,0,0,2000,68626,0,0,3509,209641,0,0,1123,25511,0,0;QS=1,0;MQSB=0.981786;MQ0F=0   PL  0,178,255
20  225091  .   A   <*> 0   .   DP=56;I16=32,24,0,0,1944,68122,0,0,3329,198841,0,0,1101,24987,0,0;QS=1,0;MQSB=0.980457;MQ0F=0   PL  0,169,255
20  225092  .   C   <*> 0   .   DP=56;I16=32,24,0,0,1867,62921,0,0,3329,198841,0,0,1079,24507,0,0;QS=1,0;MQSB=0.980457;MQ0F=0   PL  0,169,255
20  225093  .   A   <*> 0   .   DP=56;I16=32,24,0,0,1942,67998,0,0,3329,198841,0,0,1057,24071,0,0;QS=1,0;MQSB=0.980457;MQ0F=0   PL  0,169,255
20  225094  .   A   <*> 0   .   DP=55;I16=32,23,0,0,1901,66367,0,0,3269,195241,0,0,1035,23629,0,0;QS=1,0;MQSB=0.980932;MQ0F=0   PL  0,166,255
20  225095  .   A   <*> 0   .   DP=53;I16=30,23,0,0,1815,62867,0,0,3149,188041,0,0,1013,23131,0,0;QS=1,0;MQSB=0.978929;MQ0F=0   PL  0,160,255
20  225096  .   C   <*> 0   .   DP=52;I16=29,23,0,0,1750,59286,0,0,3089,184441,0,0,989,22529,0,0;QS=1,0;MQSB=0.977804;MQ0F=0    PL  0,157,255
20  225097  .   T   <*> 0   .   DP=51;I16=29,22,0,0,1826,65594,0,0,3029,180841,0,0,965,21925,0,0;QS=1,0;MQSB=0.978354;MQ0F=0    PL  0,154,255
20  225098  .   C   <*> 0   .   DP=51;I16=29,22,0,0,1744,60074,0,0,3029,180841,0,0,941,21369,0,0;QS=1,0;MQSB=0.978354;MQ0F=0    PL  0,154,255
20  225099  .   T   <*> 0   .   DP=49;I16=28,21,0,0,1753,63097,0,0,2909,173641,0,0,918,20810,0,0;QS=1,0;MQSB=0.977751;MQ0F=0    PL  0,148,255
20  225100  .   T   <*> 0   .   DP=48;I16=27,21,0,0,1688,59612,0,0,2849,170041,0,0,896,20296,0,0;QS=1,0;MQSB=0.976472;MQ0F=0    PL  0,144,255
20  225101  .   G   <*> 0   .   DP=46;I16=25,21,0,0,1543,52049,0,0,2729,162841,0,0,873,19677,0,0;QS=1,0;MQSB=0.973548;MQ0F=0    PL  0,138,255
20  225102  .   A   <*> 0   .   DP=44;I16=23,21,0,0,1488,50652,0,0,2609,155641,0,0,850,19004,0,0;QS=1,0;MQSB=0.970024;MQ0F=0    PL  0,132,255
20  225103  .   A   <*> 0   .   DP=44;I16=23,21,0,0,1531,53697,0,0,2609,155641,0,0,826,18328,0,0;QS=1,0;MQSB=0.970024;MQ0F=0    PL  0,132,255
20  225104  .   A   <*> 0   .   DP=44;I16=23,21,0,0,1497,51873,0,0,2609,155641,0,0,801,17651,0,0;QS=1,0;MQSB=0.970024;MQ0F=0    PL  0,132,255
20  225105  .   A   <*> 0   .   DP=41;I16=22,19,0,0,1430,50294,0,0,2429,144841,0,0,779,17021,0,0;QS=1,0;MQSB=0.969627;MQ0F=0    PL  0,123,255
20  225106  .   A   <*> 0   .   DP=41;I16=22,19,0,0,1441,50887,0,0,2429,144841,0,0,754,16288,0,0;QS=1,0;MQSB=0.969627;MQ0F=0    PL  0,123,255
20  225107  .   A   <*> 0   .   DP=41;I16=22,19,0,0,1413,49175,0,0,2429,144841,0,0,728,15556,0,0;QS=1,0;MQSB=0.969627;MQ0F=0    PL  0,123,255
20  225108  .   A   <*> 0   .   DP=41;I16=22,19,0,0,1363,46243,0,0,2429,144841,0,0,701,14827,0,0;QS=1,0;MQSB=0.969627;MQ0F=0    PL  0,123,255
20  225109  .   G   <*> 0   .   DP=39;I16=21,18,0,0,1278,42540,0,0,2309,137641,0,0,676,14150,0,0;QS=1,0;MQSB=0.968368;MQ0F=0    PL  0,117,255
20  225110  .   G   <*> 0   .   DP=37;I16=21,16,0,0,1262,43720,0,0,2189,130441,0,0,651,13423,0,0;QS=1,0;MQSB=0.970373;MQ0F=0    PL  0,111,255
20  225111  .   C   <*> 0   .   DP=37;I16=20,16,0,0,1211,41503,0,0,2160,129600,0,0,609,12457,0,0;QS=1,0;MQSB=1;MQ0F=0   PL  0,108,255
20  225112  .   A   <*> 0   .   DP=36;I16=21,15,0,0,1272,45466,0,0,2129,126841,0,0,602,12118,0,0;QS=1,0;MQSB=0.971458;MQ0F=0    PL  0,108,255
20  225113  .   G   <*> 0   .   DP=35;I16=21,14,0,0,1219,42685,0,0,2069,123241,0,0,579,11537,0,0;QS=1,0;MQSB=0.972604;MQ0F=0    PL  0,105,255
20  225114  .   C   <*> 0   .   DP=35;I16=21,14,0,0,1197,41303,0,0,2069,123241,0,0,556,11002,0,0;QS=1,0;MQSB=0.972604;MQ0F=0    PL  0,105,255
20  225115  .   C   <*> 0   .   DP=35;I16=20,14,0,0,1178,41150,0,0,2009,119641,0,0,515,10175,0,0;QS=1,0;MQSB=0.970446;MQ0F=0    PL  0,102,255
20  225116  .   T   <*> 0   .   DP=33;I16=19,14,0,0,1173,41877,0,0,1949,116041,0,0,493,9717,0,0;QS=1,0;MQSB=0.968015;MQ0F=0 PL  0,99,255
20  225117  .   A   <*> 0   .   DP=33;I16=19,14,0,0,1141,40007,0,0,1949,116041,0,0,471,9303,0,0;QS=1,0;MQSB=0.968015;MQ0F=0 PL  0,99,255
20  225118  .   G   <*> 0   .   DP=33;I16=19,14,0,0,1135,39339,0,0,1949,116041,0,0,447,8835,0,0;QS=1,0;MQSB=0.968015;MQ0F=0 PL  0,99,255
20  225119  .   G   <*> 0   .   DP=32;I16=18,14,0,0,1090,37658,0,0,1889,112441,0,0,424,8414,0,0;QS=1,0;MQSB=0.965264;MQ0F=0 PL  0,96,255
20  225120  .   A   <*> 0   .   DP=30;I16=16,14,0,0,1031,35929,0,0,1769,105241,0,0,401,7939,0,0;QS=1,0;MQSB=0.958545;MQ0F=0 PL  0,90,255
20  225121  .   G   <*> 0   .   DP=27;I16=15,12,0,0,918,31436,0,0,1589,94441,0,0,379,7409,0,0;QS=1,0;MQSB=0.958048;MQ0F=0   PL  0,81,255
20  225122  .   A   <*> 0   .   DP=26;I16=14,12,0,0,851,28365,0,0,1529,90841,0,0,358,6922,0,0;QS=1,0;MQSB=0.953497;MQ0F=0   PL  0,78,255
20  225123  .   A   <*> 0   .   DP=26;I16=14,12,0,0,887,30579,0,0,1529,90841,0,0,337,6477,0,0;QS=1,0;MQSB=0.953497;MQ0F=0   PL  0,78,255
20  225124  .   A   <*> 0   .   DP=25;I16=14,11,0,0,873,30767,0,0,1469,87241,0,0,316,6024,0,0;QS=1,0;MQSB=0.955682;MQ0F=0   PL  0,75,255
20  225125  .   G   <*> 0   .   DP=25;I16=14,11,0,0,824,27454,0,0,1469,87241,0,0,293,5515,0,0;QS=1,0;MQSB=0.955682;MQ0F=0   PL  0,75,255
20  225126  .   C   <*> 0   .   DP=22;I16=12,10,0,0,717,23833,0,0,1289,76441,0,0,273,5049,0,0;QS=1,0;MQSB=0.947103;MQ0F=0   PL  0,66,255
20  225127  .   A   <*> 0   .   DP=20;I16=11,9,0,0,671,22767,0,0,1169,69241,0,0,255,4621,0,0;QS=1,0;MQSB=0.943233;MQ0F=0    PL  0,60,255
20  225128  .   A   <*> 0   .   DP=19;I16=10,9,0,0,641,21917,0,0,1109,65641,0,0,238,4228,0,0;QS=1,0;MQSB=0.934728;MQ0F=0    PL  0,57,255
20  225129  .   C   <*> 0   .   DP=18;I16=9,9,0,0,589,19515,0,0,1080,64800,0,0,221,3819,0,0;QS=1,0;MQSB=1;MQ0F=0    PL  0,54,255
20  225130  .   A   <*> 0   .   DP=18;I16=8,9,0,0,584,20190,0,0,1020,61200,0,0,192,3300,0,0;QS=1,0;MQSB=1;MQ0F=0    PL  0,51,255
20  225131  .   T   <*> 0   .   DP=14;I16=6,8,0,0,482,16740,0,0,840,50400,0,0,179,2979,0,0;QS=1,0;MQSB=1;MQ0F=0 PL  0,42,255
20  225132  .   G   <*> 0   .   DP=13;I16=6,7,0,0,447,15479,0,0,780,46800,0,0,167,2683,0,0;QS=1,0;MQSB=0.961166;MQ0F=0  PL  0,39,255
20  225133  .   A   <*> 0   .   DP=13;I16=6,7,0,0,454,15926,0,0,780,46800,0,0,155,2411,0,0;QS=1,0;MQSB=0.961166;MQ0F=0  PL  0,39,255
20  225134  .   T   <*> 0   .   DP=13;I16=6,7,0,0,433,14821,0,0,780,46800,0,0,142,2114,0,0;QS=1,0;MQSB=0.961166;MQ0F=0  PL  0,39,255
20  225135  .   T   <*> 0   .   DP=11;I16=5,6,0,0,390,13926,0,0,660,39600,0,0,131,1841,0,0;QS=1,0;MQSB=0.950952;MQ0F=0  PL  0,33,255
20  225136  .   T   <*> 0   .   DP=11;I16=5,6,0,0,387,13697,0,0,660,39600,0,0,120,1590,0,0;QS=1,0;MQSB=0.950952;MQ0F=0  PL  0,33,255
20  225137  .   T   <*> 0   .   DP=11;I16=5,6,0,0,391,14009,0,0,660,39600,0,0,109,1361,0,0;QS=1,0;MQSB=0.950952;MQ0F=0  PL  0,33,255
20  225138  .   T   <*> 0   .   DP=11;I16=5,6,0,0,386,13644,0,0,660,39600,0,0,98,1154,0,0;QS=1,0;MQSB=0.950952;MQ0F=0   PL  0,33,255
20  225139  .   C   <*> 0   .   DP=11;I16=5,6,0,0,358,12000,0,0,660,39600,0,0,87,969,0,0;QS=1,0;MQSB=0.950952;MQ0F=0    PL  0,33,246
20  225140  .   A   <*> 0   .   DP=10;I16=4,6,0,0,351,12335,0,0,600,36000,0,0,77,805,0,0;QS=1,0;MQSB=1.00775;MQ0F=0 PL  0,30,243
20  225141  .   C   <*> 0   .   DP=10;I16=4,6,0,0,335,11279,0,0,600,36000,0,0,67,661,0,0;QS=1,0;MQSB=1.00775;MQ0F=0 PL  0,30,236
20  225142  .   A   <*> 0   .   DP=10;I16=4,6,0,0,343,11809,0,0,600,36000,0,0,57,537,0,0;QS=1,0;MQSB=1.00775;MQ0F=0 PL  0,30,238
20  225143  .   T   <*> 0   .   DP=9;I16=4,5,0,0,302,10172,0,0,540,32400,0,0,48,432,0,0;QS=1,0;MQSB=0.974597;MQ0F=0 PL  0,27,220
20  225144  .   A   <*> 0   .   DP=9;I16=4,5,0,0,294,9686,0,0,540,32400,0,0,39,345,0,0;QS=1,0;MQSB=0.974597;MQ0F=0  PL  0,27,216
20  225145  .   T   <*> 0   .   DP=7;I16=4,3,0,0,229,7565,0,0,420,25200,0,0,32,274,0,0;QS=1,0;MQSB=1.01283;MQ0F=0   PL  0,21,183
20  225146  .   T   <*> 0   .   DP=5;I16=2,3,0,0,174,6066,0,0,300,18000,0,0,27,215,0,0;QS=1,0;MQSB=1;MQ0F=0 PL  0,15,150
20  225147  .   T   <*> 0   .   DP=5;I16=2,3,0,0,172,5936,0,0,300,18000,0,0,22,166,0,0;QS=1,0;MQSB=1;MQ0F=0 PL  0,15,150
20  225148  .   T   <*> 0   .   DP=5;I16=2,3,0,0,164,5392,0,0,300,18000,0,0,17,127,0,0;QS=1,0;MQSB=1;MQ0F=0 PL  0,15,141
20  225149  .   A   <*> 0   .   DP=4;I16=2,2,0,0,125,3931,0,0,240,14400,0,0,13,97,0,0;QS=1,0;MQSB=1;MQ0F=0  PL  0,12,114
20  225150  .   A   <*> 0   .   DP=2;I16=1,1,0,0,69,2385,0,0,120,7200,0,0,11,73,0,0;QS=1,0;MQSB=1;MQ0F=0    PL  0,6,69
20  225151  .   C   <*> 0   .   DP=2;I16=1,1,0,0,68,2312,0,0,120,7200,0,0,9,53,0,0;QS=1,0;MQSB=1;MQ0F=0 PL  0,6,68
20  225152  .   T   <*> 0   .   DP=2;I16=1,1,0,0,70,2452,0,0,120,7200,0,0,7,37,0,0;QS=1,0;MQSB=1;MQ0F=0 PL  0,6,70
20  225153  .   T   <*> 0   .   DP=2;I16=1,1,0,0,63,2009,0,0,120,7200,0,0,5,25,0,0;QS=1,0;MQSB=1;MQ0F=0 PL  0,6,63
20  225154  .   G   <*> 0   .   DP=1;I16=1,0,0,0,34,1156,0,0,60,3600,0,0,4,16,0,0;QS=1,0;MQ0F=0 PL  0,3,34
20  225155  .   G   <*> 0   .   DP=1;I16=1,0,0,0,34,1156,0,0,60,3600,0,0,3,9,0,0;QS=1,0;MQ0F=0  PL  0,3,34
20  225156  .   T   <*> 0   .   DP=1;I16=1,0,0,0,29,841,0,0,60,3600,0,0,2,4,0,0;QS=1,0;MQ0F=0   PL  0,3,29
20  225157  .   T   <*> 0   .   DP=1;I16=1,0,0,0,26,676,0,0,60,3600,0,0,1,1,0,0;QS=1,0;MQ0F=0   PL  0,3,26
20  225158  .   T   <*> 0   .   DP=1;I16=1,0,0,0,24,576,0,0,60,3600,0,0,0,0,0,0;QS=1,0;MQ0F=0   PL  0,3,24
xubo@xubo:~/xubo/data/avocado/NA12878_snp_A2G_chr20$ bcftools

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