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input vcf file
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##fileformat=VCFv4.1
##samtoolsVersion=0.1.19-44428cd
##reference=file:///public/home/yxu/genes/genome/hg_bowtie2.fa
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr10,length=133797422>
##contig=<ID=chr11,length=135086622>
##contig=<ID=chr12,length=133275309>
##contig=<ID=chr13,length=114364328>
##contig=<ID=chr14,length=107043718>
##contig=<ID=chr15,length=101991189>
##contig=<ID=chr16,length=90338345>
##contig=<ID=chr17,length=83257441>
##contig=<ID=chr18,length=80373285>
##contig=<ID=chr19,length=58617616>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr20,length=64444167>
##contig=<ID=chr21,length=46709983>
##contig=<ID=chr22,length=50818468>
##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>
##contig=<ID=chr9,length=138394717>
##contig=<ID=chrM,length=16569>
##contig=<ID=chrX,length=156040895>
##contig=<ID=chrY,length=57227415>
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in g
roup2.">
##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
##INFO=<ID=QBD,Number=1,Type=Float,Description="Quality by Depth: QUAL/#reads">
##INFO=<ID=RPB,Number=1,Type=Float,Description="Read Position Bias">
##INFO=<ID=MDV,Number=1,Type=Integer,Description="Maximum number of high-quality nonRef reads in samples">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias (v2) for filtering splice-site artefacts in RNA-seq data. Note: this version may
be broken.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality non-reference bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /public/home/yxu/lung-seq/2/SRR493937_1/SRR493937_1.bam
chr1 89923 . A T 68 . DP=3;VDB=4.340713e-02;AF1=1;AC1=2;DP4=0,0,2,1;MQ=50;FQ=-36 GT:PL:GQ 1/1:100,9,0:16
chr1 90311 . T C 8.64 . DP=17;VDB=6.089532e-02;RPB=-2.152553e+00;AF1=0.5;AC1=1;DP4=6,7,1,2;MQ=48;FQ=11.3;PV4=1,0.15,1,
0.059 GT:PL:GQ 0/1:38,0,229:40
chr1 134223 . G C 87 . DP=5;VDB=2.649457e-02;RPB=8.293682e-01;AF1=0.5013;AC1=1;DP4=1,0,3,1;MQ=50;FQ=-5.45;PV4=1,0.42,
1,1 GT:PL:GQ 0/1:117,0,23:26
chr1 134667 . A G 158 . DP=6;VDB=7.655903e-02;AF1=1;AC1=2;DP4=0,0,3,3;MQ=50;FQ=-45 GT:PL:GQ 1/1:191,18,0:3
3
chr1 141588 . T C 25 . DP=3;VDB=7.040000e-02;RPB=8.745357e-01;AF1=0.5005;AC1=1;DP4=0,1,1,1;MQ=50;FQ=3.01;PV4=1,0.29,1
,1 GT:PL:GQ 0/1:55,0,27:30
chr1 141677 . T C 38 . DP=3;VDB=7.520000e-02;RPB=8.745357e-01;AF1=0.5003;AC1=1;DP4=1,0,1,1;MQ=50;FQ=4.77;PV4=1,0.33,1
,0.034 GT:PL:GQ 0/1:68,0,30:33
chr1 141705 . T C 75 . DP=3;VDB=5.227153e-02;AF1=1;AC1=2;DP4=0,0,2,1;MQ=50;FQ=-36 GT:PL:GQ 1/1:107,9,0:16
chr1 141715 . T C 21 . DP=4;VDB=1.760000e-02;RPB=1.111223e+00;AF1=0.5;AC1=1;DP4=1,1,1,1;MQ=50;FQ=23.8;PV4=1,0.28,1,1
GT:PL:GQ 0/1:51,0,63:54
chr1 141912 . T C 16.1 . DP=9;VDB=5.960000e-02;RPB=-8.217058e-01;AF1=0.5;AC1=1;DP4=2,5,0,2;MQ=50;FQ=19.1;PV4=1,1,1,1
GT:PL:GQ 0/1:46,0,167:49
chr1 142235 . G A 37.8 . DP=3;VDB=4.960000e-02;AF1=1;AC1=2;DP4=0,0,0,2;MQ=50;FQ=-33 GT:PL:GQ 1/1:69,6,0:10
chr1 142359 . G A 19.1 . DP=6;VDB=6.560000e-02;RPB=1.427508e+00;AF1=0.5;AC1=1;DP4=1,3,1,1;MQ=50;FQ=22;PV4=1,0.13,1,0.15
GT:PL:GQ 0/1:49,0,121:52
chr1 142678 . G A 23 . DP=6;VDB=7.680000e-02;RPB=1.427508e+00;AF1=0.5;AC1=1;DP4=2,2,0,2;MQ=50;FQ=26;PV4=0.47,0.37,1,1
GT:PL:GQ 0/1:53,0,123:56
chr1 146512 . G A 57 . DP=5;VDB=2.063840e-02;RPB=5.314005e-01;AF1=0.5;AC1=1;DP4=0,2,0,3;MQ=50;FQ=32;PV4=1,1,1,0.22
GT:PL:GQ 0/1:87,0,59:62
chr1 146692 . C T 77 . DP=3;VDB=5.498856e-02;AF1=1;AC1=2;DP4=0,0,1,2;MQ=50;FQ=-36 GT:PL:GQ 1/1:109,9,0:16
chr1 147192 . G C 115 . DP=6;VDB=9.014600e-02;RPB=8.217058e-01;AF1=0.5016;AC1=1;DP4=1,0,2,3;MQ=50;FQ=-6.18;PV4=1,0.27,
1,1 GT:PL:GQ 0/1:145,0,22:25
chr1 147212 . G A 31 . DP=4;VDB=5.960000e-02;RPB=1.111223e+00;AF1=0.5;AC1=1;DP4=1,1,0,2;MQ=50;FQ=27.8;PV4=1,1,1,0.086
GT:PL:GQ 0/1:61,0,56:58
chr1 148031 . A T 47.8 . DP=2;VDB=7.520000e-02;AF1=1;AC1=2;DP4=0,0,1,1;MQ=50;FQ=-33 GT:PL:GQ 1/1:79,6,0:10
chr1 187485 . G A 105 . DP=8;VDB=1.075274e-01;RPB=-8.141118e-01;AF1=0.5129;AC1=1;DP4=1,0,5,2;MQ=43;FQ=-14.2;PV4=1,1,0.
3,0.12 GT:PL:GQ 0/1:135,0,13:16
chr1 187497 . G A 83 . DP=10;VDB=8.228788e-02;RPB=0.000000e+00;AF1=0.5;AC1=1;DP4=4,2,2,2;MQ=45;FQ=82.5;PV4=1,1,1,1
GT:PL:GQ 0/1:113,0,112:99
chr1 492837 . T C 71 . DP=9;VDB=5.878212e-02;RPB=2.268540e-01;AF1=0.5;AC1=1;DP4=4,1,2,2;MQ=44;FQ=32;PV4=0.52,1,1,0.08
GT:PL:GQ 0/1:101,0,59:62
chr1 493191 . C T 4.77 . DP=3;VDB=5.960000e-02;RPB=8.745357e-01;AF1=0.5001;AC1=1;DP4=0,1,0,2;MQ=41;FQ=3.68;PV4=1,1,0.33
,0.12 GT:PL:GQ 0/1:33,0,30:31
chr1 495013 . G A 20 . DP=8;VDB=7.360000e-02;RPB=-1.114905e+00;AF1=0.5;AC1=1;DP4=4,2,2,0;MQ=35;FQ=22.3;PV4=1,1,1,1
GT:PL:GQ 0/1:50,0,57:52
chr1 496350 . C G 44.8 . DP=2;VDB=6.880000e-02;AF1=1;AC1=2;DP4=0,0,1,1;MQ=50;FQ=-33 GT:PL:GQ 1/1:76,6,0:10
chr1 499108 . C A 56 . DP=3;VDB=6.439972e-02;AF1=1;AC1=2;DP4=0,0,2,1;MQ=50;FQ=-36 GT:PL:GQ 1/1:88,9,0:16
chr1 629080 . C CG 202 . INDEL;IS=1,0.006135;DP=17;VDB=5.778060e-07;AF1=1;AC1=2;DP4=0,0,14,3;MQ=50;FQ=-85.5 GT:PL:
GQ 1/1:243,51,0:99
chr1 630110 . T C 222 . DP=56;VDB=2.722598e-17;AF1=1;AC1=2;DP4=0,0,38,18;MQ=50;FQ=-196 GT:PL:GQ 1/1:255,169,0:
99
chr1 630641 . A G 27 . DP=30;VDB=6.508500e-02;AF1=1;AC1=2;DP4=0,0,0,3;MQ=50;FQ=-36 GT:PL:GQ 1/1:59,9,0:16
chr1 631010 . T C 9.31 . DP=4;VDB=6.400000e-02;AF1=1;AC1=2;DP4=0,0,2,0;MQ=35;FQ=-33 GT:PL:GQ 1/1:40,6,0:8
chr1 633323 . A G 222 . DP=84;VDB=3.574446e-17;AF1=1;AC1=2;DP4=0,0,32,15;MQ=41;FQ=-168 GT:PL:GQ 1/1:255,141,0:
99
chr1 634696 . T C 222 . DP=100;VDB=4.607356e-11;AF1=1;AC1=2;DP4=0,0,21,29;MQ=50;FQ=-178 GT:PL:GQ 1/1:255,151,0:
99
chr1 634699 . C T 222 . DP=50;VDB=7.853913e-11;AF1=1;AC1=2;DP4=0,0,20,29;MQ=50;FQ=-175 GT:PL:GQ 1/1:255,148,0:
99
chr1 634714 . G A 222 . DP=78;VDB=2.426475e-20;AF1=1;AC1=2;DP4=0,0,29,36;MQ=50;FQ=-223 GT:PL:GQ 1/1:255,196,0:
99
chr1 634717 . A G 222 . DP=88;VDB=7.805137e-21;AF1=1;AC1=2;DP4=0,0,29,36;MQ=50;FQ=-223 GT:PL:GQ 1/1:255,196,0:
99
chr1 728463 . G A 12.3 . DP=8;VDB=7.520000e-02;RPB=-1.114905e+00;AF1=0.5;AC1=1;DP4=1,5,1,1;MQ=40;FQ=15.1;PV4=0.46,0.17,
1,1 GT:PL:GQ 0/1:42,0,82:44
chr1 807414 . A G 44.8 . DP=2;VDB=6.720000e-02;AF1=1;AC1=2;DP4=0,0,1,1;MQ=50;FQ=-33 GT:PL:GQ 1/1:76,6,0:10
chr1 820507 . C G 40.8 . DP=2;VDB=7.520000e-02;AF1=1;AC1=2;DP4=0,0,1,1;MQ=50;FQ=-33 GT:PL:GQ 1/1:72,6,0:10
chr1 820510 . A T 40.8 . DP=2;VDB=7.520000e-02;AF1=1;AC1=2;DP4=0,0,1,1;MQ=50;FQ=-33 GT:PL:GQ 1/1:72,6,0:10
chr1 820888 . G A 25.8 . DP=2;VDB=7.520000e-02;AF1=1;AC1=2;DP4=0,0,1,1;MQ=50;FQ=-33 GT:PL:GQ 1/1:57,6,0:10
chr1 821000 . T A 46.8 . DP=2;VDB=4.960000e-02;AF1=1;AC1=2;DP4=0,0,1,1;MQ=50;FQ=-33 GT:PL:GQ 1/1:78,6,0:10
chr1 822260 . G A 65 . DP=4;VDB=6.442004e-02;RPB=8.435450e-01;AF1=0.5004;AC1=1;DP4=1,0,2,1;MQ=50;FQ=3.55;PV4=1,0.33,1
,1 GT:PL:GQ 0/1:95,0,28:31
chr1 822354 . C T 99.5 . DP=4;VDB=6.497467e-02;AF1=1;AC1=2;DP4=0,0,2,2;MQ=50;FQ=-39 GT:PL:GQ 1/1:132,12,0:2
1
chr1 822556 . C A 30.8 . DP=2;VDB=5.280000e-02;AF1=1;AC1=2;DP4=0,0,1,1;MQ=50;FQ=-33 GT:PL:GQ 1/1:62,6,0:10
chr1 822764 . A G 27.8 . DP=2;VDB=6.720000e-02;AF1=1;AC1=2;DP4=0,0,0,2;MQ=50;FQ=-33 GT:PL:GQ 1/1:59,6,0:10
chr1 822944 . T C 19.8 . DP=2;VDB=7.840000e-02;AF1=1;AC1=2;DP4=0,0,1,1;MQ=50;FQ=-33 GT:PL:GQ 1/1:51,6,0:10
chr1 851639 . C T 48.8 . DP=2;VDB=5.920000e-02;AF1=1;AC1=2;DP4=0,0,1,1;MQ=50;FQ=-33 GT:PL:GQ 1/1:80,6,0:10
chr1 853460 . T C 93 . DP=41;VDB=1.486932e-01;RPB=4.589437e+00;AF1=0.5;AC1=1;DP4=23,5,8,4;MQ=43;FQ=96;PV4=0.41,1,0.09
9,0.025 GT:PL:GQ 0/1:123,0,228:99
chr1 853572 . G A 18.1 . DP=33;VDB=1.127164e-01;RPB=-7.706435e-01;AF1=0.5;AC1=1;DP4=11,15,0,7;MQ=44;FQ=21;PV4=0.067,0.1
6,1,1 GT:PL:GQ 0/1:48,0,255:51
chr1 853621 . G A 58 . DP=38;VDB=9.958396e-02;RPB=1.769370e+00;AF1=0.5;AC1=1;DP4=21,7,1,7;MQ=46;FQ=61;PV4=0.0026,0.2,
1,1 GT:PL:GQ 0/1:88,0,255:91