##fileformat=VCFv4.1
##samtoolsVersion=0.1.17 (r973:277)
##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.">
##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=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sn4_01
scaffold_1	306	.	A	G	140	.	DP=24;AF1=0.5;AC1=1;DP4=3,1,11,6;MQ=34;FQ=24;PV4=1,3.2e-07,1,1	GT:PL:GQ	0/1:170,0,51:54
scaffold_1	1231	.	C	T	73.5	.	DP=13;AF1=1;AC1=2;DP4=0,1,6,6;MQ=37;FQ=-29;PV4=1,3e-08,0.3,1	GT:PL:GQ	1/1:103,2,0:5
scaffold_1	1299	.	A	G	64.3	.	DP=10;AF1=0.5336;AC1=1;DP4=1,2,2,3;MQ=23;FQ=-18.1;PV4=1,0.00054,1,1	GT:PL:GQ	0/1:94,0,9:12
scaffold_1	1724	.	C	T	42	.	DP=4;AF1=1;AC1=2;DP4=0,0,1,2;MQ=28;FQ=-36	GT:PL:GQ	1/1:74,9,0:16
scaffold_1	1919	.	G	A	82.3	.	DP=6;AF1=1;AC1=2;DP4=0,0,1,4;MQ=37;FQ=-42	GT:PL:GQ	1/1:115,15,0:27
scaffold_1	1988	.	C	T	89	.	DP=10;AF1=1;AC1=2;DP4=0,0,4,5;MQ=37;FQ=-54	GT:PL:GQ	1/1:122,27,0:51
scaffold_1	2447	.	G	A	111	.	DP=37;AF1=0.5;AC1=1;DP4=2,13,10,12;MQ=28;FQ=85;PV4=0.073,0.00068,1,0.47	GT:PL:GQ	0/1:141,0,112:99
scaffold_1	2448	.	T	C	63	.	DP=37;AF1=0.5;AC1=1;DP4=11,12,1,13;MQ=28;FQ=66;PV4=0.013,1,0.011,1	GT:PL:GQ	0/1:93,0,146:96
scaffold_1	2461	.	T	C	34	.	DP=47;AF1=0.5;AC1=1;DP4=15,12,2,13;MQ=27;FQ=37;PV4=0.0097,1.8e-33,0.015,1	GT:PL:GQ	0/1:64,0,255:67
scaffold_1	2498	.	T	C	102	.	DP=42;AF1=0.5;AC1=1;DP4=19,3,15,5;MQ=26;FQ=105;PV4=0.45,2.6e-20,1,1	GT:PL:GQ	0/1:132,0,155:99
scaffold_1	2511	.	C	T	70	.	DP=54;AF1=0.5;AC1=1;DP4=12,5,15,1;MQ=25;FQ=73;PV4=0.17,8.2e-08,1,1	GT:PL:GQ	0/1:100,0,184:99
scaffold_1	2517	.	G	A	177	.	DP=59;AF1=0.5;AC1=1;DP4=12,8,27,7;MQ=26;FQ=167;PV4=0.21,1e-09,0.048,0.28	GT:PL:GQ	0/1:207,0,194:99
scaffold_1	2589	.	T	C	67	.	DP=55;AF1=0.5;AC1=1;DP4=13,15,6,16;MQ=31;FQ=70;PV4=0.24,1.2e-06,5.9e-05,1	GT:PL:GQ	0/1:97,0,255:99
scaffold_1	2977	.	C	T	13.5	.	DP=15;AF1=1;AC1=2;DP4=0,0,4,1;MQ=15;FQ=-42	GT:PL:GQ	1/1:46,15,0:23
scaffold_1	3131	.	C	T	6.2	.	DP=15;AF1=0.4999;AC1=1;DP4=3,3,3,4;MQ=14;FQ=8.21;PV4=1,1e-08,0.072,1	GT:PL:GQ	0/1:35,0,44:36
scaffold_1	3509	.	A	G	56	.	DP=23;AF1=1;AC1=2;DP4=4,0,9,9;MQ=12;FQ=-55;PV4=0.11,3.8e-11,1,1	GT:PL:GQ	1/1:89,28,0:53
scaffold_1	3687	.	T	C	150	.	DP=21;AF1=1;AC1=2;DP4=0,1,6,13;MQ=21;FQ=-74;PV4=1,0.0047,1,1	GT:PL:GQ	1/1:183,47,0:91
scaffold_1	3698	.	A	G	129	.	DP=22;AF1=1;AC1=2;DP4=1,1,6,13;MQ=19;FQ=-67;PV4=1,0.041,1,1	GT:PL:GQ	1/1:162,40,0:77
scaffold_1	3744	.	T	C	14.2	.	DP=31;AF1=0.5;AC1=1;DP4=10,13,4,4;MQ=17;FQ=17.1;PV4=1,1.6e-05,1,1	GT:PL:GQ	0/1:44,0,99:47
scaffold_1	3758	.	G	A	21	.	DP=27;AF1=0.5;AC1=1;DP4=9,6,5,4;MQ=18;FQ=24;PV4=1,2.9e-09,0.12,0.0054	GT:PL:GQ	0/1:51,0,106:54
scaffold_1	3858	.	T	C	16.1	.	DP=21;AF1=0.5;AC1=1;DP4=9,3,5,4;MQ=22;FQ=19.1;PV4=0.4,3.7e-07,1,1	GT:PL:GQ	0/1:46,0,116:49
scaffold_1	4212	.	T	C	47.5	.	DP=6;AF1=1;AC1=2;DP4=0,0,2,2;MQ=34;FQ=-39	GT:PL:GQ	1/1:80,12,0:21
scaffold_1	4251	.	G	A	95	.	DP=13;AF1=1;AC1=2;DP4=0,0,5,7;MQ=37;FQ=-63	GT:PL:GQ	1/1:128,36,0:69
scaffold_1	4326	.	G	T	48.5	.	DP=5;AF1=1;AC1=2;DP4=0,0,0,4;MQ=37;FQ=-39	GT:PL:GQ	1/1:81,12,0:21
scaffold_1	4596	.	AG	A	122	.	INDEL;DP=25;AF1=0.5;AC1=1;DP4=9,5,6,2;MQ=37;FQ=125;PV4=1,0.07,1,0.47	GT:PL:GQ	0/1:160,0,254:99
scaffold_1	4613	.	G	A	39	.	DP=27;AF1=0.5;AC1=1;DP4=10,7,7,3;MQ=37;FQ=42;PV4=0.69,1.3e-09,1,1	GT:PL:GQ	0/1:69,0,255:72
scaffold_1	4886	.	G	A	218	.	DP=20;AF1=1;AC1=2;DP4=0,0,9,11;MQ=33;FQ=-87	GT:PL:GQ	1/1:251,60,0:99
scaffold_1	4904	.	T	C	208	.	DP=24;AF1=1;AC1=2;DP4=0,0,9,11;MQ=33;FQ=-87	GT:PL:GQ	1/1:241,60,0:99
scaffold_1	5119	.	C	T	11.3	.	DP=19;AF1=0.5;AC1=1;DP4=4,3,2,1;MQ=34;FQ=14.1;PV4=1,1,0,1	GT:PL:GQ	0/1:41,0,58:43
scaffold_1	5228	.	G	A	225	.	DP=40;AF1=0.5;AC1=1;DP4=10,9,7,13;MQ=37;FQ=225;PV4=0.34,4.3e-09,0.12,1	GT:PL:GQ	0/1:255,0,255:99
scaffold_1	5397	.	G	A	223	.	DP=46;AF1=0.5;AC1=1;DP4=7,12,8,15;MQ=33;FQ=224;PV4=1,8.4e-06,9.5e-05,1	GT:PL:GQ	0/1:253,0,255:99
scaffold_1	5464	.	T	C	17.1	.	DP=46;AF1=1;AC1=2;DP4=0,0,2,1;MQ=37;FQ=-36	GT:PL:GQ	1/1:49,9,0:15
scaffold_1	5627	.	G	C	225	.	DP=42;AF1=0.5;AC1=1;DP4=7,8,12,13;MQ=36;FQ=221;PV4=1,0.0078,0.055,1	GT:PL:GQ	0/1:255,0,249:99
scaffold_1	5671	.	C	G	222	.	DP=48;AF1=1;AC1=2;DP4=0,0,20,26;MQ=36;FQ=-165	GT:PL:GQ	1/1:255,138,0:99
scaffold_1	5721	.	C	A	166	.	DP=71;AF1=0.5;AC1=1;DP4=23,28,13,5;MQ=37;FQ=169;PV4=0.059,2.4e-15,1,1	GT:PL:GQ	0/1:196,0,255:99
scaffold_1	5766	.	T	C	71	.	DP=60;AF1=0.5;AC1=1;DP4=14,4,11,7;MQ=36;FQ=74;PV4=0.47,1.3e-20,0.037,1	GT:PL:GQ	0/1:101,0,249:99
scaffold_1	5844	.	A	G,T	213	.	DP=31;AF1=1;AC1=2;DP4=0,0,13,16;MQ=31;FQ=-111	GT:PL:GQ	1/1:246,84,0,239,62,236:99
scaffold_1	5869	.	C	G	6.17	.	DP=36;AF1=1;AC1=2;DP4=0,0,0,3;MQ=33;FQ=-36	GT:PL:GQ	1/1:37,9,0:10
scaffold_1	6555	.	T	C	132	.	DP=25;AF1=0.5;AC1=1;DP4=1,3,6,11;MQ=34;FQ=22;PV4=1,4.2e-11,1,1	GT:PL:GQ	0/1:162,0,49:52
scaffold_1	14489	.	A	G	6.98	.	DP=35;AF1=0.4999;AC1=1;DP4=12,15,3,5;MQ=18;FQ=9.53;PV4=1,0.00048,1,1	GT:PL:GQ	0/1:36,0,119:37
scaffold_1	14547	.	C	T	58	.	DP=41;AF1=0.5;AC1=1;DP4=7,8,10,10;MQ=25;FQ=61;PV4=1,7.2e-11,0.0021,1	GT:PL:GQ	0/1:88,0,182:91
scaffold_1	14556	.	A	G	165	.	DP=41;AF1=0.5;AC1=1;DP4=11,4,9,15;MQ=24;FQ=106;PV4=0.048,4.7e-10,0.43,1	GT:PL:GQ	0/1:195,0,133:99
scaffold_1	14563	.	T	C	11.3	.	DP=40;AF1=0.5;AC1=1;DP4=17,12,2,8;MQ=25;FQ=14.2;PV4=0.065,0.00025,0.11,1	GT:PL:GQ	0/1:41,0,232:43
scaffold_1	14566	.	T	C	74	.	DP=38;AF1=0.5;AC1=1;DP4=10,16,7,4;MQ=26;FQ=77;PV4=0.28,4e-05,1,1	GT:PL:GQ	0/1:104,0,217:99
scaffold_1	14737	.	T	C	154	.	DP=14;AF1=1;AC1=2;DP4=1,2,3,8;MQ=29;FQ=-35;PV4=1,0.021,1,1	GT:PL:GQ	1/1:186,8,0:14
scaffold_1	14803	.	T	C	56.3	.	DP=13;AF1=0.543;AC1=1;DP4=2,3,2,3;MQ=24;FQ=-19;PV4=1,0.019,1,1	GT:PL:GQ	0/1:86,0,8:11
scaffold_1	14810	.	A	G	32.5	.	DP=10;AF1=1;AC1=2;DP4=1,2,3,3;MQ=21;FQ=-34;PV4=1,0.031,1,1	GT:PL:GQ	1/1:64,7,0:12
scaffold_1	14833	.	G	A	91	.	DP=24;AF1=0.5;AC1=1;DP4=7,3,6,8;MQ=25;FQ=92.6;PV4=0.24,7.8e-07,0.41,1	GT:PL:GQ	0/1:121,0,125:99
scaffold_1	14889	.	ATAGCACTAAAGCATT	AT	24.5	.	INDEL;DP=29;AF1=0.5;AC1=1;DP4=8,8,3,1;MQ=23;FQ=15.3;PV4=0.59,0.03,1,0.013	GT:PL:GQ	0/1:62,0,50:53
scaffold_1	14974	.	C	T	14.2	.	DP=13;AF1=0.5;AC1=1;DP4=3,6,4,0;MQ=20;FQ=17.1;PV4=0.07,0.00039,1,1	GT:PL:GQ	0/1:44,0,67:47
scaffold_1	15147	.	T	C	43.2	.	DP=5;AF1=1;AC1=2;DP4=1,0,1,3;MQ=21;FQ=-35;PV4=0.4,0.0059,1,1	GT:PL:GQ	1/1:75,8,0:14
scaffold_1	15157	.	C	T	43.2	.	DP=5;AF1=1;AC1=2;DP4=1,0,1,3;MQ=21;FQ=-35;PV4=0.4,0.0035,1,1	GT:PL:GQ	1/1:75,8,0:14
scaffold_1	15169	.	A	G	43.3	.	DP=5;AF1=1;AC1=2;DP4=0,0,2,3;MQ=21;FQ=-42	GT:PL:GQ	1/1:76,15,0:27
scaffold_1	15202	.	G	A	109	.	DP=18;AF1=1;AC1=2;DP4=0,2,2,11;MQ=27;FQ=-39;PV4=1,1,1,1	GT:PL:GQ	1/1:141,12,0:21
scaffold_1	15207	.	A	G	154	.	DP=22;AF1=1;AC1=2;DP4=2,2,5,12;MQ=25;FQ=-37;PV4=0.57,4.9e-07,1,1	GT:PL:GQ	1/1:186,10,0:17
scaffold_1	15338	.	A	G	103	.	DP=47;AF1=0.5;AC1=1;DP4=14,18,5,8;MQ=24;FQ=106;PV4=1,9.7e-10,1,1	GT:PL:GQ	0/1:133,0,187:99
scaffold_1	15688	.	T	C	41	.	DP=26;AF1=0.5;AC1=1;DP4=9,3,4,2;MQ=24;FQ=44;PV4=1,0.00017,1,1	GT:PL:GQ	0/1:71,0,116:74
scaffold_1	15734	.	C	A	41	.	DP=38;AF1=0.5;AC1=1;DP4=12,3,13,1;MQ=27;FQ=44;PV4=0.6,4.9e-26,0.0061,0.44	GT:PL:GQ	0/1:71,0,195:74
scaffold_1	15972	.	A	G	21	.	DP=22;AF1=0.5;AC1=1;DP4=5,11,1,5;MQ=19;FQ=18.6;PV4=0.63,0.19,1,0.3	GT:PL:GQ	0/1:51,0,47:49
scaffold_1	16037	.	G	A	100	.	DP=28;AF1=0.5;AC1=1;DP4=11,5,6,6;MQ=26;FQ=90.8;PV4=0.44,3e-09,1,1	GT:PL:GQ	0/1:130,0,118:99
scaffold_1	16437	.	G	A	99	.	DP=8;AF1=1;AC1=2;DP4=0,0,5,3;MQ=24;FQ=-51	GT:PL:GQ	1/1:132,24,0:45
scaffold_1	17200	.	C	T	64.1	.	DP=26;AF1=1;AC1=2;DP4=2,1,9,5;MQ=31;FQ=-28;PV4=1,0.45,0.24,1	GT:PL:GQ	1/1:93,1,0:4
scaffold_1	17257	.	G	A	145	.	DP=40;AF1=0.5;AC1=1;DP4=8,7,12,11;MQ=30;FQ=88;PV4=1,0.065,1,1	GT:PL:GQ	0/1:175,0,115:99
scaffold_1	17258	.	T	C	76	.	DP=40;AF1=0.5;AC1=1;DP4=13,11,7,7;MQ=30;FQ=79;PV4=1,0.28,1.1e-05,0.41	GT:PL:GQ	0/1:106,0,203:99
scaffold_1	17379	.	A	G	149	.	DP=10;AF1=1;AC1=2;DP4=0,0,8,2;MQ=29;FQ=-57	GT:PL:GQ	1/1:182,30,0:57
scaffold_1	17408	.	T	C	78.1	.	DP=10;AF1=0.505;AC1=1;DP4=2,0,6,2;MQ=29;FQ=-10.4;PV4=1,8.1e-08,1,1	GT:PL:GQ	0/1:108,0,17:20
scaffold_1	17423	.	A	G	42.2	.	DP=5;AF1=0.5263;AC1=1;DP4=1,0,3,1;MQ=25;FQ=-17.1;PV4=1,1,1,1	GT:PL:GQ	0/1:72,0,10:13
scaffold_1	17584	.	T	C	77.5	.	DP=9;AF1=1;AC1=2;DP4=1,1,4,3;MQ=30;FQ=-31;PV4=1,5.4e-07,1,0.065	GT:PL:GQ	1/1:108,4,0:7
scaffold_1	17590	.	C	T	103	.	DP=13;AF1=1;AC1=2;DP4=0,0,7,5;MQ=30;FQ=-63	GT:PL:GQ	1/1:136,36,0:69
scaffold_1	17611	.	C	T	12.7	.	DP=28;AF1=1;AC1=2;DP4=0,0,0,4;MQ=34;FQ=-39	GT:PL:GQ	1/1:45,12,0:18
scaffold_1	17673	.	A	G	66	.	DP=30;AF1=0.5;AC1=1;DP4=8,10,7,4;MQ=27;FQ=69;PV4=0.45,0.12,0.28,1	GT:PL:GQ	0/1:96,0,158:99
scaffold_1	17687	.	G	A	118	.	DP=16;AF1=0.5064;AC1=1;DP4=1,2,8,4;MQ=24;FQ=-11.3;PV4=0.53,0.13,1,1	GT:PL:GQ	0/1:148,0,16:19
scaffold_1	17770	.	T	C	56	.	DP=9;AF1=0.5;AC1=1;DP4=1,4,1,3;MQ=30;FQ=54.3;PV4=1,0.017,1,0.35	GT:PL:GQ	0/1:86,0,83:84
scaffold_1	17882	.	A	G	144	.	DP=27;AF1=1;AC1=2;DP4=0,2,9,10;MQ=21;FQ=-64;PV4=0.49,3.1e-08,1,0.0094	GT:PL:GQ	1/1:177,37,0:71