##fileformat=VCFv4.1
##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">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Skate_sorted.bam
Little_Skate_cDNA-0	48	.	G	A	13.9	.	DP=2;VDB=0.0076;AF1=1;AC1=2;DP4=0,0,0,2;MQ=60;FQ=-33	PL	45,6,0
Little_Skate_cDNA-0	49	.	G	A	42.8	.	DP=2;VDB=0.0076;AF1=1;AC1=2;DP4=0,0,0,2;MQ=60;FQ=-33	PL	74,6,0
Little_Skate_cDNA-0	176	.	A	G	15.9	.	DP=2;VDB=0.0076;AF1=1;AC1=2;DP4=0,0,0,2;MQ=60;FQ=-33	PL	47,6,0
Little_Skate_cDNA-0	258	.	T	G	3.02	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30	PL	30,3,0
Little_Skate_cDNA-0	275	.	T	C	16.1	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30	PL	46,3,0
Little_Skate_cDNA-0	330	.	A	G	13.9	.	DP=2;VDB=0.0013;AF1=1;AC1=2;DP4=0,0,0,2;MQ=60;FQ=-33	PL	45,6,0
Little_Skate_cDNA-0	537	.	G	T	3.02	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30	PL	30,3,0
Little_Skate_cDNA-4	56	.	A	G	32.3	.	DP=10;VDB=0.0001;AF1=0.5336;AC1=1;DP4=1,0,6,0;MQ=60;FQ=-18.1;PV4=1,0.0053,1,0	PL	62,0,9
Little_Skate_cDNA-5	1087	.	A	G	16.1	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30	PL	46,3,0
Little_Skate_cDNA-7	63	.	A	G	4.77	.	DP=6;VDB=0.0067;AF1=0.4999;AC1=1;DP4=4,0,2,0;MQ=60;FQ=6.99;PV4=1,0.11,1,1	PL	33,0,98
Little_Skate_cDNA-7	83	.	G	A	20.1	.	DP=5;VDB=0.0060;AF1=0.5;AC1=1;DP4=2,0,3,0;MQ=60;FQ=13.7;PV4=1,0.08,1,1	PL	50,0,41
Little_Skate_cDNA-7	252	.	C	A	71.1	.	DP=7;VDB=0.0018;AF1=1;AC1=2;DP4=0,0,6,0;MQ=60;FQ=-45	PL	104,18,0
Little_Skate_cDNA-7	295	.	A	G	46	.	DP=7;VDB=0.0023;AF1=0.5032;AC1=1;DP4=2,0,5,0;MQ=60;FQ=-8.63;PV4=1,1,1,1	PL	76,0,19
Little_Skate_cDNA-8	356	.	A	C	99	.	DP=12;VDB=0.0029;AF1=1;AC1=2;DP4=0,0,8,1;MQ=60;FQ=-54	PL	132,27,0
Little_Skate_cDNA-10	201	.	C	T	63.5	.	DP=4;VDB=0.0058;AF1=1;AC1=2;DP4=0,0,0,4;MQ=60;FQ=-39	PL	96,12,0
Little_Skate_cDNA-10	220	.	T	G	74.5	.	DP=4;VDB=0.0058;AF1=1;AC1=2;DP4=0,0,0,4;MQ=60;FQ=-39	PL	107,12,0
Little_Skate_cDNA-11	462	.	A	C	23.8	.	DP=2;VDB=0.0400;AF1=1;AC1=2;DP4=0,0,2,0;MQ=60;FQ=-33	PL	55,6,0
Little_Skate_cDNA-13	246	.	A	T	3.02	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30	PL	30,3,0
Little_Skate_cDNA-17	183	.	A	G	9.53	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30	PL	39,3,0
Little_Skate_cDNA-19	92	.	G	A	3.02	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30	PL	30,3,0
Little_Skate_cDNA-19	165	.	C	T	3.02	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30	PL	30,3,0
Little_Skate_cDNA-22	455	.	G	A	8.64	.	DP=5;VDB=0.0052;AF1=0.5;AC1=1;DP4=0,3,0,2;MQ=60;FQ=11.3;PV4=1,0.39,1,1	PL	38,0,59
Little_Skate_cDNA-23	129	.	A	T	74.1	.	DP=6;VDB=0.0010;AF1=1;AC1=2;DP4=0,0,0,6;MQ=60;FQ=-45	PL	107,18,0
Little_Skate_cDNA-23	137	.	A	G	41.5	.	DP=6;VDB=0.0017;AF1=0.5718;AC1=1;DP4=0,1,0,5;MQ=60;FQ=-21;PV4=1,1,1,1	PL	71,0,6
Little_Skate_cDNA-23	146	.	G	C	78.1	.	DP=6;VDB=0.0010;AF1=1;AC1=2;DP4=0,0,0,6;MQ=60;FQ=-45	PL	111,18,0
Little_Skate_cDNA-24	56	.	A	C	39	.	DP=3;VDB=0.0000;AF1=1;AC1=2;DP4=0,0,3,0;MQ=60;FQ=-36	PL	71,9,0
Little_Skate_cDNA-26	508	.	G	A	11.3	.	DP=4;VDB=0.0035;AF1=0.5;AC1=1;DP4=0,2,0,2;MQ=60;FQ=11.3;PV4=1,0.39,1,1	PL	41,0,41
Little_Skate_cDNA-27	385	.	T	G	14.2	.	DP=2;AF1=0.5032;AC1=1;DP4=1,0,1,0;MQ=60;FQ=-8.64;PV4=1,1,1,1	PL	44,0,19
Little_Skate_cDNA-27	1180	.	C	T	12	.	DP=2;VDB=0.0007;AF1=1;AC1=2;DP4=0,0,2,0;MQ=60;FQ=-33	PL	43,6,0
Little_Skate_cDNA-28	140	.	C	A	135	.	DP=16;VDB=0.0001;AF1=1;AC1=2;DP4=0,0,14,1;MQ=60;FQ=-72	PL	168,45,0
Little_Skate_cDNA-28	181	.	G	T	136	.	DP=14;VDB=0.0000;AF1=1;AC1=2;DP4=0,0,11,1;MQ=60;FQ=-63	PL	169,36,0
Little_Skate_cDNA-28	428	.	A	G	85.3	.	DP=12;VDB=0.0072;AF1=1;AC1=2;DP4=1,0,11,0;MQ=60;FQ=-42;PV4=1,1,1,0.39	PL	118,15,0
Little_Skate_cDNA-28	572	.	A	T	85.1	.	DP=7;VDB=0.0020;AF1=1;AC1=2;DP4=0,0,7,0;MQ=60;FQ=-48	PL	118,21,0
Little_Skate_cDNA-28	618	.	T	C	49.1	.	DP=7;VDB=0.0020;AF1=1;AC1=2;DP4=0,0,7,0;MQ=60;FQ=-48	PL	82,21,0
Little_Skate_cDNA-28	670	.	G	A	76	.	DP=9;VDB=0.0015;AF1=1;AC1=2;DP4=0,0,9,0;MQ=60;FQ=-54	PL	109,27,0
Little_Skate_cDNA-28	1021	.	G	A	9.52	.	DP=12;VDB=0.0054;AF1=0.5;AC1=1;DP4=6,1,3,0;MQ=60;FQ=12.3;PV4=1,0.2,1,1	PL	39,0,163
Little_Skate_cDNA-28	1178	.	G	A	96	.	DP=10;VDB=0.0061;AF1=1;AC1=2;DP4=0,0,10,0;MQ=60;FQ=-57	PL	129,30,0
Little_Skate_cDNA-28	1223	.	C	A	66	.	DP=9;VDB=0.0042;AF1=1;AC1=2;DP4=0,0,8,0;MQ=60;FQ=-51	PL	99,24,0
Little_Skate_cDNA-28	1483	.	T	C	16.9	.	DP=2;VDB=0.0046;AF1=1;AC1=2;DP4=0,0,2,0;MQ=60;FQ=-33	PL	48,6,0
Little_Skate_cDNA-28	1672	.	C	T	4.13	.	DP=3;AF1=0.4999;AC1=1;DP4=2,0,1,0;MQ=60;FQ=6.04;PV4=1,1,1,1	PL	32,0,45
Little_Skate_cDNA-29	422	.	A	G	22.8	.	DP=2;VDB=0.0055;AF1=1;AC1=2;DP4=0,0,0,2;MQ=60;FQ=-33	PL	54,6,0
Little_Skate_cDNA-30	25	.	T	C	90	.	DP=20;VDB=0.0000;AF1=1;AC1=2;DP4=0,0,0,18;MQ=60;FQ=-81	PL	123,54,0
Little_Skate_cDNA-30	26	.	G	A	100	.	DP=20;VDB=0.0000;AF1=1;AC1=2;DP4=0,0,0,18;MQ=60;FQ=-81	PL	133,54,0
Little_Skate_cDNA-30	54	.	G	A	112	.	DP=18;VDB=0.0000;AF1=1;AC1=2;DP4=0,0,0,18;MQ=60;FQ=-81	PL	145,54,0
Little_Skate_cDNA-30	178	.	A	G	3.54	.	DP=15;VDB=0.0094;AF1=0.4998;AC1=1;DP4=0,12,0,3;MQ=60;FQ=5.47;PV4=1,0.26,1,1	PL	31,0,165
Little_Skate_cDNA-30	211	.	G	A	122	.	DP=15;VDB=0.0017;AF1=1;AC1=2;DP4=0,0,0,12;MQ=60;FQ=-63	PL	155,36,0
Little_Skate_cDNA-31	105	.	G	T	17.1	.	DP=17;VDB=0.0001;AF1=0.5;AC1=1;DP4=13,0,4,0;MQ=60;FQ=20.1;PV4=1,1,1,1	PL	47,0,130
Little_Skate_cDNA-33	70	.	C	A	71.1	.	DP=8;VDB=0.0001;AF1=1;AC1=2;DP4=0,0,0,7;MQ=60;FQ=-48	PL	104,21,0
Little_Skate_cDNA-33	101	.	C	T	70	.	DP=12;VDB=0.0002;AF1=0.5;AC1=1;DP4=0,3,0,9;MQ=60;FQ=25;PV4=1,0.035,1,0.18	PL	100,0,52
Little_Skate_cDNA-33	214	.	C	T	17.1	.	DP=20;VDB=0.0014;AF1=0.5;AC1=1;DP4=0,14,0,6;MQ=60;FQ=20.1;PV4=1,2.6e-05,1,1	PL	47,0,191
Little_Skate_cDNA-33	243	.	G	A	58	.	DP=29;VDB=0.0109;AF1=0.5;AC1=1;DP4=0,19,0,10;MQ=60;FQ=61;PV4=1,0.2,1,1	PL	88,0,120
Little_Skate_cDNA-33	276	.	T	C	118	.	DP=34;VDB=0.0082;AF1=1;AC1=2;DP4=0,0,0,32;MQ=60;FQ=-123	PL	151,96,0
Little_Skate_cDNA-33	471	.	C	T	80	.	DP=32;VDB=0.0081;AF1=0.5;AC1=1;DP4=0,7,0,25;MQ=60;FQ=24;PV4=1,0.47,1,1	PL	110,0,51
Little_Skate_cDNA-33	499	.	T	A	40	.	DP=29;VDB=0.0029;AF1=0.5;AC1=1;DP4=0,15,0,11;MQ=60;FQ=43;PV4=1,2e-06,1,0.44	PL	70,0,131
Little_Skate_cDNA-33	512	.	A	T	83	.	DP=28;VDB=0.0089;AF1=0.5;AC1=1;DP4=0,12,0,16;MQ=60;FQ=86;PV4=1,3.9e-15,1,0.2	PL	113,0,204
Little_Skate_cDNA-33	876	.	G	T	22	.	DP=26;VDB=0.0070;AF1=0.5;AC1=1;DP4=0,17,0,8;MQ=60;FQ=25;PV4=1,0.00032,1,1	PL	52,0,118
Little_Skate_cDNA-33	1016	.	G	A	61	.	DP=28;VDB=0.0058;AF1=0.5;AC1=1;DP4=0,17,0,10;MQ=60;FQ=63.4;PV4=1,1,1,1	PL	91,0,99
Little_Skate_cDNA-33	1452	.	C	T	60.6	.	DP=7;VDB=0.0009;AF1=0.5939;AC1=1;DP4=0,1,0,6;MQ=60;FQ=-22;PV4=1,1,1,1	PL	90,0,5
Little_Skate_cDNA-34	250	.	A	G	12.3	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30	PL	42,3,0
Little_Skate_cDNA-37	71	.	C	A	24	.	DP=6;VDB=0.0000;AF1=0.5;AC1=1;DP4=0,3,0,3;MQ=60;FQ=26.9;PV4=1,0.1,1,1	PL	54,0,69
Little_Skate_cDNA-37	109	.	C	T	36	.	DP=3;VDB=0.0000;AF1=1;AC1=2;DP4=0,0,0,3;MQ=60;FQ=-36	PL	68,9,0
Little_Skate_cDNA-37	148	.	C	T	46	.	DP=3;VDB=0.0000;AF1=1;AC1=2;DP4=0,0,0,3;MQ=60;FQ=-36	PL	78,9,0
Little_Skate_cDNA-37	468	.	T	A	16.9	.	DP=2;VDB=0.0071;AF1=1;AC1=2;DP4=0,0,0,2;MQ=60;FQ=-33	PL	48,6,0
Little_Skate_cDNA-37	633	.	G	C	36	.	DP=5;VDB=0.0134;AF1=1;AC1=2;DP4=0,0,0,3;MQ=60;FQ=-36	PL	68,9,0
Little_Skate_cDNA-37	760	.	C	T	31.1	.	DP=4;VDB=0.0036;AF1=0.505;AC1=1;DP4=0,1,0,3;MQ=60;FQ=-10.4;PV4=1,0.41,1,1	PL	61,0,17
Little_Skate_cDNA-38	135	.	T	C	66	.	DP=9;VDB=0.0000;AF1=0.5004;AC1=1;DP4=2,0,7,0;MQ=60;FQ=3.55;PV4=1,0.27,1,0.31	PL	96,0,28
Little_Skate_cDNA-39	680	.	A	G	3.02	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30	PL	30,3,0
Little_Skate_cDNA-39	747	.	C	T	7.8	.	DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30	PL	37,3,0
Little_Skate_cDNA-40	365	.	T	A	12.3	.	DP=1;AF1=1;AC1=2;DP4=0,0,0,1;MQ=60;FQ=-30	PL	42,3,0
Little_Skate_cDNA-41	142	.	A	G	8.44	.	DP=2;VDB=0.0070;AF1=1;AC1=2;DP4=0,0,0,2;MQ=60;FQ=-33	PL	39,6,0
Little_Skate_cDNA-42	421	.	C	T	55.5	.	DP=4;VDB=0.0007;AF1=1;AC1=2;DP4=0,0,0,4;MQ=60;FQ=-39	PL	88,12,0
Little_Skate_cDNA-42	567	.	A	G	14.9	.	DP=2;VDB=-0.0025;AF1=1;AC1=2;DP4=0,0,0,2;MQ=60;FQ=-33	PL	46,6,0
Little_Skate_cDNA-46	132	.	G	A	11.3	.	DP=3;AF1=0.5;AC1=1;DP4=0,2,0,1;MQ=60;FQ=12.5;PV4=1,1,1,0	PL	41,0,44