##fileformat=VCFv4.1
###samtoolsVersion=0.1.19-44428cd
###reference=file://genome/ICSASG_v2-scf.fna
##contig=<ID=CM003279.1,length=159038749>
##contig=<ID=CM003280.1,length=72943711>
##contig=<ID=CM003281.1,length=92503428>
##contig=<ID=CM003282.1,length=82398023>
##contig=<ID=CM003283.1,length=80503876>
##contig=<ID=CM003284.1,length=87043187>
##contig=<ID=CM003285.1,length=58785265>
##contig=<ID=CM003286.1,length=26434011>
##contig=<ID=CM003287.1,length=141712163>
##contig=<ID=CM003288.1,length=116138521>
##contig=<ID=CM003289.1,length=93888508>
##contig=<ID=CM003290.1,length=91880962>
##contig=<ID=CM003291.1,length=107758822>
##contig=<ID=CM003292.1,length=93901823>
##contig=<ID=CM003293.1,length=103963436>
##contig=<ID=CM003294.1,length=87796322>
##contig=<ID=CM003295.1,length=57682537>
##contig=<ID=CM003296.1,length=70695409>
##contig=<ID=CM003297.1,length=82978132>
##contig=<ID=CM003298.1,length=86795997>
##contig=<ID=CM003299.1,length=58021487>
##contig=<ID=CM003300.1,length=63420196>
##contig=<ID=CM003301.1,length=49854004>
##contig=<ID=CM003302.1,length=48650976>
##contig=<ID=CM003303.1,length=51481326>
##contig=<ID=CM003304.1,length=47900953>
##contig=<ID=CM003305.1,length=43943985>
##contig=<ID=CM003306.1,length=39600944>
##contig=<ID=CM003307.1,length=42488238>
##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 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=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">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A102	A10	C7	C9	C_A_03	CB7	CB8	CB9	CC53	CD-13	CE32	CE33	CE35	CF40	CF41	C_G_03	CG26	D14	D45	G7
CM003279.1	1274	C	A	999	.	DP=154;VDB=7.295659e-02;RPB=4.492375e-01;AF1=0.1029;AC1=4;DP4=63,72,6,6;MQ=60;FQ=999;PV4=1,1,1,0.43	GT:PL:DP:SP:GQ	0/1:109,0,187:11:0:99
CM003279.1	3637	A	C	157	.	DP=116;VDB=1.265695e-01;RPB=-5.258772e-01;AF1=0.07761;AC1=3;DP4=53,51,9,1;MQ=60;FQ=157;PV4=0.021,0.0031,1,1	GT:PL:DP:SP:GQ	./.:0,6,74:2:0:14
CM003279.1	3788	GCCCC	GCCCCC	130	.	INDEL;IS=8,0.888889;DP=133;VDB=5.146828e-01;AF1=0.0754;AC1=3;DP4=57,55,4,7;MQ=60;FQ=130;PV4=0.53,1,0.005,1	GT:PL:DP:SP:GQ	0/0:0,27,128:9:0:35
CM003279.1	3879	A	C	999	.	DP=121;VDB=1.495689e-01;RPB=-1.814048e-01;AF1=0.1913;AC1=8;DP4=46,51,10,12;MQ=60;FQ=999;PV4=1,1,1,1	GT:PL:DP:SP:GQ	0/0:0,12,138:4:0:15
CM003279.1	4356	GTTTTT	GTTTTTT	41.2	.	INDEL;IS=4,0.571429;DP=105;VDB=1.545428e-01;AF1=0.09405;AC1=4;DP4=38,47,5,4;MQ=60;FQ=41.6;PV4=0.73,1,1,0.053	GT:PL:DP:SP:GQ	0/0:0,15,82:5:0:22
CM003279.1	5120	T	G	999	.	DP=134;VDB=1.582720e-01;RPB=3.041863e-01;AF1=0.1275;AC1=5;DP4=43,70,6,12;MQ=60;FQ=999;PV4=0.8,1,1,1	GT:PL:DP:SP:GQ	0/0:0,18,180:6:0:23
CM003279.1	5272	C	T	999	.	DP=126;VDB=1.443477e-01;RPB=-6.605860e-01;AF1=0.1172;AC1=5;DP4=61,50,7,5;MQ=60;FQ=999;PV4=1,0.027,1,0.32	GT:PL:DP:SP:GQ	0/0:0,24,225:8:0:30
CM003279.1	6382	A	G	71.3	.	DP=121;VDB=7.791483e-02;RPB=-3.759770e-01;AF1=0.02664;AC1=1;DP4=65,50,1,3;MQ=60;FQ=71.4;PV4=0.32,1,1,1	GT:PL:DP:SP:GQ	0/1:114,0,96:7:3:99
CM003279.1	6569	C	T	157	.	DP=135;VDB=1.148150e-01;RPB=2.755091e-01;AF1=0.05949;AC1=2;DP4=54,68,4,3;MQ=60;FQ=157;PV4=0.7,1,1,1	GT:PL:DP:SP:GQ	0/0:0,15,167:5:0:24
CM003279.1	6630	C	T	72.4	.	DP=125;VDB=2.497123e-02;RPB=1.741760e+00;AF1=0.05756;AC1=2;DP4=51,63,1,4;MQ=60;FQ=72.7;PV4=0.38,0.057,1,0.39	GT:PL:DP:SP:GQ	0/0:0,18,191:6:0:27
CM003279.1	7185	AG	A	63.8	.	INDEL;IS=4,0.571429;DP=100;VDB=5.037854e-01;AF1=0.0272;AC1=1;DP4=40,50,1,3;MQ=60;FQ=63.9;PV4=0.63,0.0022,1,0.35	GT:PL:DP:SP:GQ	0/1:114,0,53:6:4:72
CM003279.1	8490	G	T	999	.	DP=149;VDB=3.526582e-01;RPB=-4.676541e-01;AF1=0.3101;AC1=12;DP4=52,37,26,25;MQ=59;FQ=999;PV4=0.48,0.1,1,1	GT:PL:DP:SP:GQ	0/0:0,21,210:7:0:22
CM003279.1	8706	C	A	96.2	.	DP=133;VDB=3.878872e-02;RPB=-9.043283e-01;AF1=0.02613;AC1=1;DP4=49,75,5,1;MQ=57;FQ=96.3;PV4=0.081,0.079,0.078,0.021	GT:PL:DP:SP:GQ	0/0:0,30,255:10:0:43
CM003279.1	8766	G	C	999	.	DP=124;VDB=1.709482e-01;RPB=-7.952446e-01;AF1=0.1038;AC1=4;DP4=50,57,6,9;MQ=53;FQ=999;PV4=0.78,0.26,0.1,1	GT:PL:DP:SP:GQ	0/0:0,18,179:6:0:24
CM003279.1	11562	TTGCCATTCCCACTGCC	TTGCC	122	.	INDEL;IS=3,0.600000;DP=138;VDB=4.329562e-01;AF1=0.05094;AC1=2;DP4=66,60,2,2;MQ=56;FQ=122;PV4=1,0.42,1,1	GT:PL:DP:SP:GQ	0/1:36,0,205:5:0:26
CM003279.1	12325	A	T	999	.	DP=144;VDB=1.976499e-01;RPB=1.509420e+00;AF1=0.8488;AC1=34;DP4=10,9,45,61;MQ=57;FQ=999;PV4=0.46,0.077,0.0012,1	GT:PL:DP:SP:GQ	0/1:73,0,139:8:7:83
CM003279.1	12481	G	A	999	.	DP=130;VDB=3.923331e-01;RPB=6.999030e-01;AF1=0.8776;AC1=35;DP4=6,11,41,62;MQ=60;FQ=999;PV4=0.79,0.07,1,1	GT:PL:DP:SP:GQ	0/1:146,0,149:12:0:99
CM003279.1	12887	G	T	54.2	.	DP=108;VDB=6.200772e-03;RPB=-3.223527e+00;AF1=0.1082;AC1=4;DP4=47,52,0,6;MQ=59;FQ=54.7;PV4=0.032,0.13,5.3e-61,1	GT:PL:DP:SP:GQ	0/1:30,0,144:8:3:24
CM003279.1	12963	TCCTAC	TC	999	.	INDEL;IS=3,1.000000;DP=108;VDB=4.754337e-01;AF1=0.05857;AC1=2;DP4=52,42,4,1;MQ=60;FQ=999;PV4=0.38,0.14,1,1	GT:PL:DP:SP:GQ	0/0:0,12,214:4:0:21
CM003279.1	13678	C	T	94.7	.	DP=96;VDB=8.127598e-02;RPB=-1.058333e+00;AF1=0.05937;AC1=2;DP4=47,43,2,3;MQ=60;FQ=94.9;PV4=0.67,0.44,1,1	GT:PL:DP:SP:GQ	0/0:0,6,79:2:0:15
CM003279.1	14206	T	A	145	.	DP=109;VDB=1.119593e-01;RPB=8.817302e-01;AF1=0.1183;AC1=5;DP4=40,54,4,5;MQ=60;FQ=145;PV4=1,0.39,1,1	GT:PL:DP:SP:GQ	0/0:0,9,80:3:0:15
CM003279.1	14299	A	G	999	.	DP=107;VDB=1.432828e-01;RPB=1.150073e+00;AF1=0.1276;AC1=5;DP4=37,53,2,9;MQ=59;FQ=999;PV4=0.2,1,2e-13,1	GT:PL:DP:SP:GQ	0/0:0,24,226:8:0:29
CM003279.1	14548	T	C	999	.	DP=95;VDB=1.143805e-01;RPB=-2.044075e+00;AF1=0.118;AC1=4;DP4=40,41,5,3;MQ=58;FQ=999;PV4=0.71,0.081,1,0.27	GT:PL:DP:SP:GQ	./.:0,6,69:2:0:12
CM003279.1	15028	T	A	66.2	.	DP=135;VDB=1.201506e-01;RPB=-2.162342e+00;AF1=0.08537;AC1=3;DP4=68,57,8,0;MQ=52;FQ=66.6;PV4=0.01,0.3,1e-05,1	GT:PL:DP:SP:GQ	0/0:0,21,216:7:0:28
CM003279.1	15263	G	A	40.6	.	DP=140;VDB=1.315928e-02;RPB=-2.648238e+00;AF1=0.08695;AC1=4;DP4=67,62,1,7;MQ=49;FQ=40.9;PV4=0.062,0.14,0.0018,0.048	GT:PL:DP:SP:GQ	./.:13,0,190:9:0:7
CM003279.1	16038	G	T	46.2	.	DP=102;VDB=7.384173e-02;RPB=-1.514480e-01;AF1=0.09682;AC1=4;DP4=33,51,3,2;MQ=54;FQ=46.7;PV4=0.39,0.073,3.6e-06,1	GT:PL:DP:SP:GQ	0/1:55,0,31:3:0:42
CM003279.1	16346	G	C	999	.	DP=136;VDB=1.171652e-01;RPB=7.771622e-01;AF1=0.4276;G3=0.164,0.836,1.17e-06;HWE=0.00114;AC1=17;DP4=37,46,32,17;MQ=40;FQ=999;PV4=0.03,1,1,1	GT:PL:DP:SP:GQ	0/1:86,0,36:5:0:40
CM003279.1	16411	C	A	999	.	DP=141;VDB=4.962733e-06;RPB=4.287454e+00;AF1=0.3241;G3=0.358,0.642,1.448e-06;HWE=0.0199;AC1=13;DP4=35,79,18,5;MQ=40;FQ=999;PV4=3.3e-05,0.26,1,0.17	GT:PL:DP:SP:GQ	0/0:0,21,184:7:0:21
CM003279.1	16611	T	A	999	.	DP=165;VDB=9.934666e-02;RPB=-7.532254e-01;AF1=0.2779;AC1=11;DP4=73,48,23,15;MQ=56;FQ=999;PV4=1,1,0.31,1	GT:PL:DP:SP:GQ	0/1:87,0,152:9:6:86
CM003279.1	16939	G	T	999	.	DP=147;VDB=5.288363e-02;RPB=3.564616e-01;AF1=0.1256;AC1=5;DP4=74,62,5,4;MQ=60;FQ=999;PV4=1,0.41,1,1	GT:PL:DP:SP:GQ	0/1:48,0,188:9:0:43
CM003279.1	17119	A	T	158	.	DP=222;VDB=2.026237e-03;RPB=-4.510201e+00;AF1=0.09557;AC1=4;DP4=132,74,7,3;MQ=59;FQ=158;PV4=1,1,0.0021,3.3e-05	GT:PL:DP:SP:GQ	./.:15,0,151:8:0:9
CM003279.1	17203	CACATTACATTACATTACATTACATTACAACACATTACATTACATTACATTACAACACATTACATTACATTACATTA	CACATTACATTACATTACATTACAACACATTACATTACATTACATTACAACACATTACATTACATTACATTA	92.9	.	INDEL;IS=2,0.222222;DP=198;VDB=4.020615e-01;AF1=0.111;AC1=4;DP4=68,57,5,3;MQ=58;FQ=93.4;PV4=0.73,2.1e-10,2.4e-25,1	GT:PL:DP:SP:GQ	0/0:0,21,255:7:0:27
CM003279.1	17280	AAACACATTACAACACATTACAACACATTACA	AAACACATTACAACACATTACA	999	.	INDEL;IS=6,0.500000;DP=227;VDB=4.223352e-01;AF1=0.2387;AC1=10;DP4=61,70,8,10;MQ=56;FQ=999;PV4=1,1,7.5e-10,1	GT:PL:DP:SP:GQ	0/1:92,0,255:11:3:90
CM003279.1	17377	ATACATTACATTACATTACATTACATTA	ATACATTACATTACATTACATTA	999	.	INDEL;IS=12,0.800000;DP=262;VDB=2.374454e-02;AF1=0.3381;AC1=14;DP4=67,73,21,35;MQ=57;FQ=999;PV4=0.21,2e-12,0.0001,1	GT:PL:DP:SP:GQ	0/0:0,24,255:8:0:24
CM003279.1	17562	T	A	999	.	DP=161;VDB=2.263459e-02;RPB=3.636386e-01;AF1=0.4254;G3=0.1257,0.8743,2.264e-40;HWE=0.000128;AC1=17;DP4=43,50,27,27;MQ=43;FQ=999;PV4=0.73,1,0.047,1	GT:PL:DP:SP:GQ	0/1:205,0,52:10:0:56
CM003279.1	17622	A	T	76.7	.	DP=179;VDB=1.320207e-02;RPB=2.754391e+00;AF1=0.1183;AC1=5;DP4=70,89,6,6;MQ=45;FQ=77.3;PV4=0.77,3.3e-05,0.00075,1	GT:PL:DP:SP:GQ	0/0:0,30,226:10:0:36