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##fileformat=VCFv4.1
##SnpEffCmd="SnpEff -no-downstream -no-upstream WS220.66 "
##samtoolsVersion=0.1.18 (r982:295)
##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=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 group2.">
##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=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
##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=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=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )'">
##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT DA1606.bam DA1607.bam DA1608.bam DA1609.bam DA1610.bam DA1611.bam DA1612.bam DA1613.bam DA1614.bam
chr2 3321973 . G GN 104.00 . AC1=2;AC=2;AF1=1;AN=2;DP4=0,4,28,51;DP=100;EFF=FRAME_SHIFT(HIGH||-/N|-167?|187|Y46D2A.2|protein_coding|CODING|Y46D2A.2|4),UTR_5_PRIME(MODIFIER||||191|Y46D2A.5|protein_coding|CODING|Y46D2A.5|3);FQ=-222;INDEL;MQ=14;PV4=0.29,1,1,1;SF=8;VDB=0.0355 GT:GQ:PL . . . . . . . . 1/1:99:145,187,0
chr2 3796933 . T G,A 33.75 . AC1=2;AC=8,0;AF1=1;AN=8;DP4=163,248,422,991;DP=2183;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cGa|L369R|1360|Y8A9A.2|protein_coding|CODING|Y8A9A.2|);FQ=-154;MQ=10;PV4=0.014,0.12,1,1;SF=1,4,6,7;VDB=0.0252 GT:GQ:PL . 1/1:99:63,127,0,.,.,. . . 1/1:99:64,77,0,.,.,. . 1/1:99:67,103,0,.,.,. 1/1:99:.,168,0,76,195,72 .
chr2 3796996 . T C 49.00 . AC1=2;AC=2;AF1=1;AN=2;DP4=6,3,28,60;DP=113;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L390P|1360|Y8A9A.2|protein_coding|CODING|Y8A9A.2|);FQ=-168;MQ=10;PV4=0.062,0.34,0.37,0.067;SF=7;VDB=0.0038 GT:GQ:PL . . . . . . . 1/1:99:82,141,0 .
chr2 3797023 . T C,A 42.50 . AC1=2;AC=12,0;AF1=1;AN=12;DP4=1,2,51,69;DP=187;EFF=DOWNSTREAM(MODIFIER||||158|Y8A9A.3|protein_coding|CODING|Y8A9A.3|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cAg|L399Q|1360|Y8A9A.2|protein_coding|CODING|Y8A9A.2|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L399P|1360|Y8A9A.2|protein_coding|CODING|Y8A9A.2|),UPSTREAM(MODIFIER||||282|fbxb-99|protein_coding|CODING|Y8A9A.5|),UPSTREAM(MODIFIER|||||Y8A9A.1|pseudogene|NON_CODING|Y8A9A.1|);FQ=-65;MQ=11;PV4=0.33,0.032,0.41,1;SF=3,4,5,6,7,8;VDB=0.0374 GT:GQ:PL . . . 1/1:68:68,38,0,68,16,61 1/1:56:71,30,0,.,.,. 1/1:87:72,51,0,77,34,71 1/1:87:81,46,0,.,.,. 1/1:80:80,42,0,.,.,. 1/1:99:81,84,0,85,57,77
chr2 3797275 . T A 42.00 . AC1=2;AC=6;AF1=1;AN=6;DP4=18,41,34,219;DP=422;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cAg|L483Q|1360|Y8A9A.2|protein_coding|CODING|Y8A9A.2|);FQ=-104;MQ=10;PV4=0.49,1,0.16,1;SF=2,5,6;VDB=0.0381 GT:GQ:PL . . 1/1:99:70,77,0 . . 1/1:99:89,113,0 1/1:99:66,79,0 . .
chr2 4199686 . C T 67.50 . AC1=2;AC=2;AF1=1;AN=2;DP4=0,1,5,5;DP=27;EFF=INTRON(MODIFIER||||1091|cpna-1|protein_coding|CODING|F31D5.3a|5),INTRON(MODIFIER||||1107|cpna-1|protein_coding|CODING|F31D5.3b|5),INTRON(MODIFIER||||799|cpna-1|protein_coding|CODING|F31D5.3d.1|5),INTRON(MODIFIER||||799|cpna-1|protein_coding|CODING|F31D5.3d.2|5),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G697E|1788|F31D5.5|protein_coding|CODING|F31D5.5|);FQ=-34;MQ=43;PV4=1,0.029,0.36,1;SF=0;VDB=0.0268 GT:GQ:PL 1/1:12:99,7,0 . . . . . . . .
chr2 6084917 . AG AGG 54.36 . AC1=2;AC=14;AF1=1;AN=14;DP4=0,0,80,71;DP=164;EFF=FRAME_SHIFT(HIGH||-/C|-288?|667|ptc-2|protein_coding|CODING|F21H12.4|2);FQ=-88.5;INDEL;MQ=12;SF=2,3,4,5,6,7,8;VDB=0.0328 GT:GQ:PL . . 1/1:96:86,54,0 1/1:99:98,69,0 1/1:69:102,36,0 1/1:99:103,120,0 1/1:99:95,63,0 1/1:63:83,33,0 1/1:99:97,78,0
chr2 6225620 . C T 148.00 . AC1=2;AC=2;AF1=1;AN=2;DP4=0,0,12,9;DP=26;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G201E|350|C30B5.7|protein_coding|CODING|C30B5.7|);FQ=-90;MQ=44;SF=2;VDB=0.0381 GT:GQ:PL . . 1/1:99:181,63,0 . . . . . .
chr2 6535294 . GA G 214.00 . AC1=2;AC=2;AF1=1;AN=2;DP4=0,0,17,13;DP=37;EFF=FRAME_SHIFT(HIGH||-|-669|680|abcx-1|protein_coding|CODING|C56E6.1|11),INTRON(MODIFIER||||1081|C56E6.9|protein_coding|CODING|C56E6.9|3);FQ=-125;INDEL;MQ=43;SF=2;VDB=0.0217 GT:GQ:PL . . 1/1:99:255,90,0 . . . . . .
chr2 6736493 . G GC 132.00 . AC1=2;AC=2;AF1=1;AN=2;DP4=0,0,6,6;DP=29;EFF=FRAME_SHIFT(HIGH||-/C|-94?|139|T14B4.2|protein_coding|CODING|T14B4.2|2);FQ=-70.5;INDEL;MQ=44;SF=8;VDB=0.0362 GT:GQ:PL . . . . . . . . 1/1:69:173,36,0
chr2 6759926 . A AT 74.05 . AC1=2;AC=4;AF1=1;AN=4;DP4=0,0,8,7;DP=30;EFF=FRAME_SHIFT(HIGH||-/T|-189?|320|F41G3.2|protein_coding|CODING|F41G3.2|3);FQ=-61.5;INDEL;MQ=43;SF=2,5;VDB=0.0243 GT:GQ:PL . . 1/1:51:125,27,0 . . 1/1:33:104,18,0 . . .
chr2 7124007 . G GN 188.00 . AC1=2;AC=2;AF1=1;AN=2;DP4=0,0,20,9;DP=36;EFF=FRAME_SHIFT(HIGH||-/N|-129?|240|F10E7.2|protein_coding|CODING|F10E7.2|4);FQ=-122;INDEL;MQ=26;SF=5;VDB=0.0362 GT:GQ:PL . . . . . 1/1:99:229,87,0 . . .
chr2 7602964 . G A 212.00 . AC1=2;AC=2;AF1=1;AN=2;DP4=0,1,24,17;DP=46;EFF=DOWNSTREAM(MODIFIER||||304|R07G3.6|protein_coding|CODING|R07G3.6|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E979K|1316|npp-21|protein_coding|CODING|R07G3.3c|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E979K|1982|npp-21|protein_coding|CODING|R07G3.3a|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E979K|1987|npp-21|protein_coding|CODING|R07G3.3b|),UPSTREAM(MODIFIER||||284|pgam-5|protein_coding|CODING|R07G3.5.1|),UPSTREAM(MODIFIER||||284|pgam-5|protein_coding|CODING|R07G3.5.2|);FQ=-119;MQ=44;PV4=0.43,0.00035,1,1;SF=3;VDB=0.0316 GT:GQ:PL . . . 1/1:99:245,92,0 . . . . .
chr2 7697417 . G GC 117.00 . AC1=2;AC=2;AF1=1;AN=2;DP4=0,0,11,11;DP=56;EFF=FRAME_SHIFT(HIGH||-/G|-275?|729|B0495.5|protein_coding|CODING|B0495.5.1|5),FRAME_SHIFT(HIGH||-/G|-275?|729|B0495.5|protein_coding|CODING|B0495.5.2|5);FQ=-101;INDEL;MQ=44;SF=8;VDB=0.0370 GT:GQ:PL . . . . . . . . 1/1:99:158,66,0
chr2 7698901 . CG CGG 122.29 . AC1=2;AC=16;AF1=1;AN=16;DP4=0,0,44,34;DP=200;EFF=FRAME_SHIFT(HIGH||-/C|-26?|87|B0495.6|protein_coding|CODING|B0495.6|1);FQ=-49.5;INDEL;MQ=43;SF=0,1,2,3,5,6,7,8;VDB=0.0086 GT:GQ:PL 1/1:27:111,15,0 1/1:33:129,18,0 1/1:57:161,30,0 1/1:69:199,36,0 . 1/1:57:144,30,0 1/1:69:193,36,0 1/1:63:155,33,0 1/1:69:213,36,0
chr2 9863955 . C T 210.67 . AC1=2;AC=6;AF1=1;AN=6;DP4=1,1,24,47;DP=78;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A89T|107|C08H9.4|protein_coding|CODING|C08H9.4a.1|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A89T|107|C08H9.4|protein_coding|CODING|C08H9.4a.2|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A89T|465|C08H9.4|protein_coding|CODING|C08H9.4b|);FQ=-70;MQ=35;PV4=1,1,1,1;SF=0,2,8;VDB=0.0252 GT:GQ:PL 1/1:83:246,43,0 . 1/1:99:255,87,0 . . . . . 1/1:81:230,42,0
chr2 9863978 . A G 203.00 . AC1=2;AC=6;AF1=1;AN=6;DP4=0,1,25,47;DP=77;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M81T|107|C08H9.4|protein_coding|CODING|C08H9.4a.1|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M81T|107|C08H9.4|protein_coding|CODING|C08H9.4a.2|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M81T|465|C08H9.4|protein_coding|CODING|C08H9.4b|);FQ=-76;MQ=35;PV4=1,0.42,0.21,0.31;SF=0,2,8;VDB=0.0303 GT:GQ:PL 1/1:95:245,49,0 . 1/1:99:255,99,0 . . . . . 1/1:69:208,36,0
chr2 9864002 . A G 144.67 . AC1=2;AC=6;AF1=1;AN=6;DP4=0,1,23,42;DP=68;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L73P|107|C08H9.4|protein_coding|CODING|C08H9.4a.1|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L73P|107|C08H9.4|protein_coding|CODING|C08H9.4a.2|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L73P|465|C08H9.4|protein_coding|CODING|C08H9.4b|);FQ=-68;MQ=33;PV4=1,0.0053,0.17,0.34;SF=0,2,8;VDB=0.0278 GT:GQ:PL 1/1:79:172,41,0 . 1/1:99:224,90,0 . . . . . 1/1:63:137,33,0
chr2 11882734 . G C 222.00 . AC1=2;AC=4;AF1=1;AN=4;DP4=0,0,59,49;DP=111;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aCa|R42T|212|ZK930.5|protein_coding|CODING|ZK930.5|);FQ=-90;MQ=44;SF=2,8;VDB=0.0167 GT:GQ:PL . . 1/1:99:255,63,0 . . . . . 1/1:99:255,255,0
chr2 12329850 . ATTTTTTTT ATTTTTTTTT 58.17 . AC1=2;AC=6;AF1=1;AN=6;DP4=0,1,52,40;DP=119;EFF=FRAME_SHIFT(HIGH||-/T|-210?|363|sre-55|protein_coding|CODING|C50E10.7|1);FQ=-85.5;INDEL;MQ=43;PV4=0.42,1,0.45,0.3;SF=0,2,8;VDB=0.0381 GT:GQ:PL 1/1:96:91,51,0 . 1/1:99:105,51,0 . . . . . 1/1:99:100,160,0
chr2 12329854 . T TN 59.50 . AC1=2;AC=2;AF1=1;AN=2;DP4=0,1,34,24;DP=73;EFF=FRAME_SHIFT(HIGH||-/N|-209?|363|sre-55|protein_coding|CODING|C50E10.7|1);FQ=-195;INDEL;MQ=44;PV4=0.42,1,0.45,1;SF=8;VDB=0.0381 GT:GQ:PL . . . . . . . . 1/1:99:100,160,0
chr2 12471066 . A T 222.00 . AC1=2;AC=2;AF1=1;AN=2;DP4=1,0,16,31;DP=63;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V25D|231|F15A4.5|protein_coding|CODING|F15A4.5|);FQ=-145;MQ=44;PV4=0.35,1,0.43,0.25;SF=6;VDB=0.0355 GT:GQ:PL . . . . . . 1/1:99:255,118,0 . .
chr2 12607640 . A AN 214.00 . AC1=2;AC=4;AF1=1;AN=4;DP4=0,0,71,58;DP=142;EFF=FRAME_SHIFT(HIGH||-/N|-137?|274|Y38E10A.8|protein_coding|CODING|Y38E10A.8|3);FQ=-170;INDEL;MQ=44;SF=5,8;VDB=0.0374 GT:GQ:PL . . . . . 1/1:99:255,135,0 . . 1/1:99:255,253,0
chr2 12668790 . G GN 214.00 . AC1=2;AC=2;AF1=1;AN=2;DP4=0,0,29,46;DP=96;EFF=FRAME_SHIFT(HIGH||-/N|-7?|234|rgs-4|protein_coding|CODING|Y38E10A.21|1);FQ=-261;INDEL;MQ=44;SF=8;VDB=0.0384 GT:GQ:PL . . . . . . . . 1/1:99:255,226,0
chr2 12677434 . T G,C 141.00 . AC1=2;AC=2,0;AF1=1;AN=2;DP4=0,0,10,16;DP=28;EFF=DOWNSTREAM(MODIFIER|||||Y38E10A.30|ncRNA|NON_CODING|Y38E10A.30|),DOWNSTREAM(MODIFIER|||||Y38E10A.31|ncRNA|NON_CODING|Y38E10A.31|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N83T|153|Y38E10A.23|protein_coding|CODING|Y38E10A.23|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N83S|153|Y38E10A.23|protein_coding|CODING|Y38E10A.23|),UPSTREAM(MODIFIER||||305|Y38E10A.22|protein_coding|CODING|Y38E10A.22|),UPSTREAM(MODIFIER||||397|Y46G5A.2|protein_coding|CODING|Y46G5A.2|),UPSTREAM(MODIFIER||||68|Y38E10A.24|protein_coding|CODING|Y38E10A.24.1|),UPSTREAM(MODIFIER||||68|Y38E10A.24|protein_coding|CODING|Y38E10A.24.2|),UPSTREAM(MODIFIER|||||Y38E10A.t1|tRNA|NON_CODING|Y38E10A.t1|);FQ=-102;MQ=44;SF=3;VDB=0.0319 GT:GQ:PL . . . 1/1:99:174,75,0,167,55,164 . . . . .
chr2 13344908 . A G 183.00 . AC1=2;AC=2;AF1=1;AN=2;DP4=0,0,16,29;DP=47;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F141L|376|Y48C3A.11|protein_coding|CODING|Y48C3A.11.1|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F141L|376|Y48C3A.11|protein_coding|CODING|Y48C3A.11.2|);FQ=-162;MQ=33;SF=6;VDB=0.0337 GT:GQ:PL . . . . . . 1/1:99:216,135,0 . .
|
