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annotate test-data/vcf_homhet.vcf @ 8:13b6ad2ddace

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SnpEffect v3.2
author Jim Johnson <jj@umn.edu>
date Mon, 13 May 2013 12:45:07 -0500
parents b26a1aff7f81
children
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1 ##fileformat=VCFv4.0
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2 ##samtoolsVersion=0.1.15 (r949:203)
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3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
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4 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
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5 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
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6 ##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
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7 ##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele">
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8 ##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
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9 ##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
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10 ##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">
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11 ##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
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12 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
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13 ##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
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14 ##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
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15 ##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
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16 ##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
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17 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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18 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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19 ##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
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20 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
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21 ##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
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22 ##FORMAT=<ID=PL,Number=.,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
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23 ##source_20110319.1=/wsu/home/eq/eq83/eq8302/tools/vcftools/bin//vcf-merge s_1_ACAGTGA.vcf.gz s_1_CAGATCA.vcf.gz s_1_CGATGTA.vcf.gz s_1_CTTGTAA.vcf.gz s_1_GCCAATA.vcf.gz s_1_TGACCAA.vcf.gz
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24 ##sourceFiles_20110319.1=0:s_1_ACAGTGA.vcf.gz,1:s_1_CAGATCA.vcf.gz,2:s_1_CGATGTA.vcf.gz,3:s_1_CTTGTAA.vcf.gz,4:s_1_GCCAATA.vcf.gz,5:s_1_TGACCAA.vcf.gz
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25 ##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
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26 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes">
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27 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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28 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s_1_ACAGTGA_sort.bam s_1_CAGATCA_sort.bam s_1_CGATGTA_sort.bam s_1_CTTGTAA_sort.bam s_1_GCCAATA_sort.bam s_1_TGACCAA_sort.bam
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29 Y 3718196 . C T 7.59 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=4.617e-16,8.575e-07,1;MQ=39;SF=1 GT:GQ:PL . 1/1:61:38,6,0 . . . .
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30 Y 3720217 . A G 8.65 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,1;DP=2;FQ=-30;G3=4.415e-15,5.291e-06,1;MQ=38;SF=5 GT:GQ:PL . . . . . 1/1:53:38,3,0
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31 Y 3720581 . A G 7.80 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,1,0;DP=1;FQ=-30;G3=5.56e-15,5.291e-06,1;MQ=44;SF=1 GT:GQ:PL . 1/1:53:37,3,0 . . . .
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32 Y 3721154 . A G 13.90 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=9.194e-17,8.566e-07,1;MQ=37;SF=3 GT:GQ:PL . . . 1/1:61:45,6,0 . .
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33 Y 3721230 . C G 21.80 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-33;G3=1.456e-17,8.564e-07,1;MQ=29;SF=3 GT:GQ:PL . . . 1/1:61:53,6,0 . .
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34 Y 3744605 . C A 3.98 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-33;G3=1.468e-15,8.599e-07,1;MQ=19;SF=2 GT:GQ:PL . . 1/1:61:33,6,0 . . .
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35 Y 4433091 . T C 11.10 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=1.835e-16,8.568e-07,1;MQ=23;SF=5 GT:GQ:PL . . . . . 1/1:61:42,6,0
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36 Y 9945223 . ATTT ATTTT 19.80 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=2.906e-18,8.564e-07,1;INDEL;MQ=45;SF=0,2 GT:GQ:PL 1/1:61:60,6,0 . 1/1:61:57,6,0 . . .
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37 Y 9987395 . TTAT TT 80.40 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,1,2;DP=3;FQ=-43.5;G3=5.464e-26,5.886e-08,1;INDEL;MQ=43;SF=5 GT:GQ:PL . . . . . 1/1:72:120,9,0
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38 Y 10011604 . C CTT 119.17 . AC=12;AF1=1;AN=12;CI95=1,1;DP4=0,0,7,0;DP=9;FQ=-55.5;G3=4.948e-32,3.15e-11,1;INDEL;MQ=33;SF=0,1,2,3,4,5 GT:GQ:PL 1/1:99:139,21,0 1/1:96:134,24,0 1/1:99:168,36,0 1/1:99:159,45,0 1/1:99:185,33,0 1/1:99:175,39,0
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39 Y 10011748 . GAAAAAA GAAAAAAA 23.70 . AC=6;AF1=0.5;AN=12;CI95=0.5,0.5;DP4=12,12,11,10;DP=51;FQ=33.5;G3=1.256e-14,1,1.991e-19;INDEL;MQ=33;PV4=1,0.49,0.012,0.2;SF=0,1,2,3,4,5 GT:GQ:PL 0/0:71:68,0,92 1/1:55:52,0,77 1/1:71:69,0,75 1/1:69:66,0,79 1/1:56:53,0,80 1/1:62:59,0,98
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40 Y 10011894 . ATTATTTATTT ATTATTT 58.62 . AC=4;AF1=0.5;AN=8;CI95=0.5,0.5;DP4=4,11,0,6;DP=34;FQ=32.5;G3=1.991e-14,1,7.924e-52;INDEL;MQ=35;PV4=0.28,0.049,0.14,0.2;SF=1,3,4,5 GT:GQ:PL . 0/0:70:67,0,254 . 1/1:99:152,0,255 1/1:83:80,0,255 1/1:89:86,0,255
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41 Y 10011930 . ACT A 90.85 . AC=2;AF1=0.5;AN=4;CI95=0.5,0.5;DP4=2,6,1,3;DP=17;FQ=16.6;G3=3.155e-11,1,1.991e-34;INDEL;MQ=35;PV4=1,0.00044,0.33,1;SF=0,5 GT:GQ:PL 0/0:54:51,0,167 . . . . 0/0:99:206,0,255
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42 Y 10011935 . C CT 83.83 . AC=3;AF1=0.5;AN=6;CI95=0.5,0.5;DP4=1,8,2,5;DP=23;FQ=90.3;G3=1.256e-28,1,5e-26;INDEL;MQ=39;PV4=0.55,1,0.15,1;SF=1,2,4 GT:GQ:PL . 0/0:99:138,0,125 1/1:92:89,0,148 . 1/1:99:138,0,171 .
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43 Y 10011966 . ATT AT 79.38 . AC=6;AF1=0.5;AN=12;CI95=0.5,0.5;DP4=1,6,0,2;DP=14;FQ=5.09;G3=1.991e-12,1,1.256e-28;INDEL;MQ=38;PV4=1,1,0.46,0.088;SF=0,1,2,3,4,5 GT:GQ:PL 1/1:41:38,0,92 1/1:76:73,0,109 1/1:99:181,0,109 1/1:99:114,0,103 1/1:99:139,0,171 1/1:99:155,0,144
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44 Y 10028061 . CA CAA 28.40 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,2,1;DP=9;FQ=-43.5;G3=2.739e-22,5.886e-08,1;INDEL;MQ=37;SF=4,5 GT:GQ:PL . . . . 1/1:72:83,9,0 0/0:61:52,6,0
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45 Y 10029194 . CA C 73.47 . AC=10;AF1=0.7304;AN=12;CI95=0.5,1;DP4=2,0,7,3;DP=19;FQ=-32.5;G3=2.922e-150,0.9991,0.000854;INDEL;MQ=25;PV4=1,0.4,1,0.23;SF=0,1,2,3,4,5 GT:GQ:PL 0/0:3:93,0,2 1/1:85:100,17,0 1/1:99:181,36,0 1/1:90:107,18,0 1/1:3:104,0,2 1/1:70:90,10,0
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46 Y 10029452 . CAA CAAA 7.26 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,4,0;DP=13;FQ=-46.5;G3=2.341e-18,6.106e-08,1;INDEL;MQ=26;SF=3,4 GT:GQ:PL . . . 1/1:72:50,12,0 1/1:72:42,12,0 .
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47 Y 10037877 . GCCC GCCCC 14.40 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=3;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=2 GT:GQ:PL . . 1/1:61:53,6,0 . . .
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48 Y 13266272 . TTTT TTTTATTT 51.50 . AC=1;AF1=0.5;AN=2;CI95=0.5,0.5;DP4=5,1,7,0;DP=15;FQ=54.5;G3=7.924e-19,1,3.155e-24;INDEL;MQ=30;PV4=0.46,1,0.078,0.00035;SF=3 GT:GQ:PL . . . 0/0:92:89,0,116 . .
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49 Y 13268110 . GC GCC 3.66 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-40.5;G3=2.911e-16,8.571e-07,1;INDEL;MQ=23;SF=2 GT:GQ:PL . . 1/1:61:40,6,0 . . .
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50 Y 13292082 . TCCCCCCCCCC TCCCCCCC 14.40 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=3 GT:GQ:PL . . . 1/1:61:53,6,0 . .
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51 Y 13297070 . AGGTGGTGGTGGT AGGTGGTGGT 12.70 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,1;DP=1;FQ=-37.5;G3=2.782e-16,5.287e-06,1;INDEL;MQ=50;SF=5 GT:GQ:PL . . . . . 1/1:53:50,3,0
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52 Y 13312198 . CGGGGG CGGGG 14.87 . AC=5;AF1=1;AN=6;CI95=0.5,1;DP4=2,0,10,0;DP=12;FQ=-43.5;G3=1.373e-19,5.886e-08,1;INDEL;MQ=24;PV4=1,0.44,1,0.019;SF=1,4,5 GT:GQ:PL . 1/1:72:56,9,0 . . 1/1:70:57,10,0 1/1:44:48,0,42
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53 Y 13312608 . CA CAA 22.50 . AC=1;AF1=0.5032;AN=2;CI95=0.5,0.5;DP4=2,0,7,0;DP=16;FQ=-15.6;G3=4.937e-25,1,1.272e-08;INDEL;MQ=24;PV4=1,1,0.093,1;SF=2 GT:GQ:PL . . 0/0:22:60,0,19 . . .
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54 Y 13402810 . TAGAGA TAGA 29.80 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,1,1;DP=2;FQ=-40.5;G3=7.299e-19,8.564e-07,1;INDEL;MQ=33;SF=0,2 GT:GQ:PL 1/1:61:66,6,0 . 1/1:72:72,9,0 . . .
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55 Y 21153016 . AG ATG 213.83 . AC=12;AF1=1;AN=12;CI95=1,1;DP4=0,0,6,9;DP=15;FQ=-79.5;G3=7.905e-54,1e-18,1;INDEL;MQ=43;SF=0,1,2,3,4,5 GT:GQ:PL 1/1:99:255,45,0 1/1:99:.,.,0 1/1:99:255,87,0 1/1:99:.,.,0 1/1:99:255,78,0 1/1:99:.,.,0
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56 Y 21153067 . CCA C 46.50 . AC=1;AF1=0.5;AN=2;CI95=0.5,0.5;DP4=8,4,5,0;DP=18;FQ=49.5;G3=7.924e-18,1,5e-52;INDEL;MQ=39;PV4=0.26,0.08,0.035,1;SF=3 GT:GQ:PL . . . 0/0:87:84,0,255 . .
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57 Y 26325233 . TGAGAGAGAGAGA TGAGAGAGAGA 22.20 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-40.5;G3=2.308e-18,8.564e-07,1;INDEL;MQ=33;SF=0 GT:GQ:PL 1/1:61:61,6,0 . . . . .
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58 Y 28588049 . ACATCAT ACAT 7.35 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,1,0;DP=1;FQ=-37.5;G3=1.108e-15,5.288e-06,1;INDEL;MQ=44;SF=1,3 GT:GQ:PL . 1/1:53:44,3,0 . 1/1:53:44,3,0 . .
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59 Y 59030478 . AAAACAAACAAACAAACAAACAAACAAA AAAACAAACAAACAAA 14.40 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=2 GT:GQ:PL . . 1/1:61:53,6,0 . . .
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60 Y 59032947 . GTT GTTT 28.20 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=5.798e-19,8.564e-07,1;INDEL;MQ=37;SF=5 GT:GQ:PL . . . . . 1/1:61:67,6,0