##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20190323
##source=freeBayes v1.2.0-dirty
##reference=reference/ref.fa
##contig=<ID=Chromosome,length=4411532>
##phasing=none
##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-1495044"
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
##bcftools_viewVersion=1.9+htslib-1.9
##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Sat Mar 23 06:45:26 2019
##bcftools_annotateVersion=1.9+htslib-1.9
##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Sat Mar 23 06:45:26 2019
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	out
Chromosome	1849	.	C	A	3412.24	.	AB=0.0;AO=110;DP=110;QA=3850;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:110:0:0:110:3850:-346.644,-33.1133,0.0
Chromosome	1977	.	A	G	3234.43	.	AB=0.0;AO=106;DP=106;QA=3704;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:106:0:0:106:3704:-333.508,-31.9092,0.0
Chromosome	4013	.	T	C	3965.91	.	AB=0.0;AO=125;DP=125;QA=4448;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:125:0:0:125:4448:-400.411,-37.6288,0.0
Chromosome	7362	.	G	C	4009.71	.	AB=0.0;AO=126;DP=126;QA=4518;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4518:-406.711,-37.9298,0.0
Chromosome	9304	.	G	A	4222.23	.	AB=0.0;AO=136;DP=136;QA=4764;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:136:0:0:136:4764:-428.865,-40.9401,0.0
Chromosome	11820	.	C	G	2252.54	.	AB=0.0;AO=74;DP=74;QA=2662;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:74:0:0:74:2662:-239.791,-22.2762,0.0
Chromosome	11879	.	A	G	1815.99	.	AB=0.0;AO=63;DP=63;QA=2212;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:63:0:0:63:2212:-199.306,-18.9649,0.0
Chromosome	14785	.	T	C	4342.4	.	AB=0.0;AO=139;DP=139;QA=4874;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:139:0:0:139:4874:-438.763,-41.8432,0.0
Chromosome	14861	.	G	T	4237.79	.	AB=0.0;AO=133;DP=135;QA=4758;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:135:0:0:133:4758:-427.969,-40.037,0.0
Chromosome	15117	.	C	G	3298.26	.	AB=0.0;AO=106;DP=106;QA=3708;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:106:0:0:106:3708:-333.903,-31.9092,0.0
Chromosome	15890	.	G	A	3349.13	.	AB=0.0;AO=116;DP=117;QA=3770;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:117:0:0:116:3770:-339.321,-34.9195,0.0
Chromosome	16119	.	C	A	3794.09	.	AB=0.0;AO=124;DP=125;QA=4268;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:125:0:0:124:4268:-383.905,-37.3277,0.0
Chromosome	21795	.	G	A	768.571	.	AB=0.0;AO=28;DP=28;QA=892;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:892:-80.5646,-8.42884,0.0
Chromosome	25610	.	G	C	2779.82	.	AB=0.0;AO=89;DP=89;QA=3137;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:89:0:0:89:3137:-282.515,-26.7917,0.0
Chromosome	26959	.	C	G	2791.1	.	AB=0.0;AO=91;DP=91;QA=3152;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:91:0:0:91:3152:-283.856,-27.3937,0.0
Chromosome	27455	.	T	C	1646.76	.	AB=0.0;AO=52;DP=52;QA=1868;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:52:0:0:52:1868:-168.374,-15.6536,0.0
Chromosome	28366	.	AT	A	2447.14	.	AB=0.0;AO=82;DP=84;QA=2764;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:84:0:0:82:2764:-248.651,-24.6845,0.0
Chromosome	34044	.	T	C	3866.76	.	AB=0.0;AO=122;DP=122;QA=4351;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:122:0:0:122:4351:-391.712,-36.7257,0.0
Chromosome	36008	.	G	C	2942.73	.	AB=0.0;AO=98;DP=101;QA=3356;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:101:0:0:98:3356:-301.935,-29.5009,0.0
Chromosome	37031	.	C	G	3922.6	.	AB=0.0;AO=128;DP=129;QA=4437;QR=34;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:129:1:34:128:4437:-396.072,-35.434,0.0
Chromosome	37305	.	C	G	4975.87	.	AB=0.0;AO=157;DP=157;QA=5577;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:157:0:0:157:5577:-501.976,-47.2617,0.0
Chromosome	39158	.	C	G	2017.05	.	AB=0.0;AO=66;DP=66;QA=2297;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:66:0:0:66:2297:-206.967,-19.868,0.0
Chromosome	42281	.	C	A	996.941	.	AB=0.0;AO=33;DP=33;QA=1179;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1179:-106.407,-9.93399,0.0
Chromosome	42967	.	G	C	2851.59	.	AB=0.0;AO=92;DP=92;QA=3244;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:92:0:0:92:3244:-292.146,-27.6948,0.0
Chromosome	43347	.	T	C	2847.24	.	AB=0.0;AO=92;DP=92;QA=3233;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:92:0:0:92:3233:-291.161,-27.6948,0.0
Chromosome	44768	.	A	G	3099.48	.	AB=0.0;AO=99;DP=99;QA=3501;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:99:0:0:99:3501:-315.241,-29.802,0.0
Chromosome	49360	.	C	T	2971.13	.	AB=0.0;AO=97;DP=97;QA=3365;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:97:0:0:97:3365:-303.059,-29.1999,0.0
Chromosome	49690	.	GCC	G	3479.85	.	AB=0.0;AO=117;DP=117;QA=3917;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:117:0:0:117:3917:-352.709,-35.2205,0.0
Chromosome	50557	.	T	C	3743.4	.	AB=0.0;AO=121;DP=121;QA=4203;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:121:0:0:121:4203:-378.409,-36.4246,0.0
Chromosome	51949	.	A	G	3521.52	.	AB=0.0;AO=112;DP=112;QA=3955;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:112:0:0:112:3955:-356.092,-33.7154,0.0
Chromosome	54394	.	A	G	3304.32	.	AB=0.0;AO=104;DP=105;QA=3711;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:104:3711:-333.937,-31.3071,0.0
Chromosome	62049	.	A	G	2249.46	.	AB=0.0;AO=77;DP=78;QA=2659;QR=35;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:78:1:35:77:2659:-236.018,-19.9817,0.0
Chromosome	63146	.	G	T	5120.15	.	AB=0.0;AO=163;DP=163;QA=5737;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:163:0:0:163:5737:-516.376,-49.0679,0.0
Chromosome	65150	.	C	T	4046.85	.	AB=0.0;AO=134;DP=134;QA=4538;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:134:0:0:134:4538:-408.565,-40.338,0.0
Chromosome	65246	.	C	T	3297.8	.	AB=0.0;AO=106;DP=107;QA=3712;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:107:0:0:106:3712:-334.038,-31.9092,0.0
Chromosome	68337	.	T	TC	1791.13	.	AB=0.0;AO=60;DP=61;QA=2038;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:61:0:0:60:2038:-183.378,-18.0618,0.0
Chromosome	69989	.	G	A	3539.46	.	AB=0.0;AO=119;DP=119;QA=3973;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:119:0:0:119:3973:-357.725,-35.8226,0.0
Chromosome	70267	.	G	T	3018.85	.	AB=0.0;AO=100;DP=101;QA=3421;QR=25;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:101:1:25:100:3421:-305.576,-27.9042,0.0
Chromosome	70816	.	A	G	4198.57	.	AB=0.0;AO=136;DP=136;QA=4707;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:136:0:0:136:4707:-423.747,-40.9401,0.0
Chromosome	71336	.	G	C	556.161	.	AB=0.0;AO=21;DP=21;QA=770;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:770:-69.6143,-6.32163,0.0
Chromosome	71914	.	T	C	3905.06	.	AB=0.0;AO=126;DP=126;QA=4382;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4382:-394.523,-37.9298,0.0
Chromosome	75233	.	C	A	1903.61	.	AB=0.0;AO=64;DP=64;QA=2172;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:64:0:0:64:2172:-195.723,-19.2659,0.0
Chromosome	75940	.	G	C	2674.83	.	AB=0.0;AO=89;DP=89;QA=3048;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:89:0:0:89:3048:-274.519,-26.7917,0.0
Chromosome	87468	.	C	T	4061.4	.	AB=0.0;AO=126;DP=126;QA=4584;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:126:0:0:126:4584:-412.628,-37.9298,0.0
Chromosome	92199	.	T	G	686.38	.	AB=0.0;AO=23;DP=23;QA=799;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:799:-72.2155,-6.92369,0.0
Chromosome	94388	.	G	A	2922.87	.	AB=0.0;AO=95;DP=95;QA=3292;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:95:0:0:95:3292:-296.486,-28.5979,0.0
Chromosome	99162	.	TCGGTGTGCG	T	2040.99	.	AB=0.0;AO=78;DP=78;QA=2358;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:78:0:0:78:2358:-212.453,-23.4803,0.0
Chromosome	105139	.	C	A	3418.74	.	AB=0.0;AO=109;DP=110;QA=3888;QR=38;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:110:1:38:109:3888:-346.257,-29.316,0.0
Chromosome	105736	.	T	C	1805.18	.	AB=0.0;AO=61;DP=61;QA=2101;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:61:0:0:61:2101:-189.335,-18.3628,0.0
Chromosome	116000	.	T	G	3196.37	.	AB=0.0;AO=105;DP=105;QA=3605;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:105:3605:-324.628,-31.6082,0.0
Chromosome	122109	.	A	G	3324.29	.	AB=0.0;AO=111;DP=111;QA=3735;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:111:0:0:111:3735:-336.329,-33.4143,0.0
Chromosome	123454	.	C	T	4362.28	.	AB=0.0;AO=136;DP=137;QA=4894;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:137:0:0:136:4894:-440.321,-40.9401,0.0
Chromosome	123520	.	T	C	3793.13	.	AB=0.0;AO=121;DP=121;QA=4262;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:121:0:0:121:4262:-383.682,-36.4246,0.0
Chromosome	125711	.	GGTT	G	3140.7	.	AB=0.0;AO=105;DP=105;QA=3531;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:105:0:0:105:3531:-317.98,-31.6082,0.0
Chromosome	125830	.	G	GA	2079.98	.	AB=0.0;AO=69;DP=72;QA=2347;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:69:2347:-211.164,-20.7711,0.0
Chromosome	131174	.	T	TG	2854.04	.	AB=0.0;AO=97;DP=99;QA=3213;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:99:0:0:97:3213:-288.972,-29.1999,0.0
Chromosome	133839	.	C	T	2457.55	.	AB=0.0;AO=78;DP=78;QA=2802;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:78:0:0:78:2802:-252.374,-23.4803,0.0
Chromosome	134024	.	T	C	2242.53	.	AB=0.0;AO=72;DP=72;QA=2543;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:72:2543:-229.099,-21.6742,0.0
Chromosome	138419	.	G	A	4166.36	.	AB=0.0;AO=132;DP=132;QA=4683;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:132:0:0:132:4683:-421.582,-39.736,0.0
Chromosome	139297	.	G	T	3706.81	.	AB=0.0;AO=120;DP=120;QA=4165;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:120:0:0:120:4165:-374.978,-36.1236,0.0
Chromosome	143207	.	T	C	2180.95	.	AB=0.0;AO=72;DP=72;QA=2523;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:72:0:0:72:2523:-227.3,-21.6742,0.0
Chromosome	146087	.	T	C	4315.28	.	AB=0.0;AO=137;DP=137;QA=4844;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:137:0:0:137:4844:-436.07,-41.2411,0.0
Chromosome	147262	.	G	T	3766.49	.	AB=0.0;AO=122;DP=122;QA=4228;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:122:0:0:122:4228:-380.649,-36.7257,0.0
Chromosome	154283	.	T	C	4403.08	.	AB=0.0;AO=141;DP=141;QA=4941;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:141:0:0:141:4941:-444.791,-42.4452,0.0
Chromosome	154990	.	G	T	4207.92	.	AB=0.0;AO=142;DP=143;QA=4724;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:143:0:0:142:4724:-424.969,-42.7463,0.0
Chromosome	162151	.	GT	G	2208.67	.	AB=0.0;AO=81;DP=84;QA=2524;QR=0;RO=0;TYPE=del	GT:DP:RO:QR:AO:QA:GL	1/1:84:0:0:81:2524:-226.95,-24.3834,0.0
Chromosome	163940	.	A	G	2507.97	.	AB=0.0;AO=80;DP=80;QA=2839;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:80:0:0:80:2839:-255.719,-24.0824,0.0
Chromosome	166253	.	A	C	3141.13	.	AB=0.0;AO=102;DP=102;QA=3586;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:102:0:0:102:3586:-322.902,-30.7051,0.0
Chromosome	177857	.	G	A	2984.02	.	AB=0.0;AO=98;DP=98;QA=3389;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:98:0:0:98:3389:-305.192,-29.5009,0.0
Chromosome	188800	.	T	C	1887.67	.	AB=0.0;AO=64;DP=64;QA=2217;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:64:0:0:64:2217:-199.772,-19.2659,0.0
Chromosome	190816	.	A	C	1715.49	.	AB=0.0;AO=57;DP=57;QA=2026;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:57:0:0:57:2026:-182.579,-17.1587,0.0
Chromosome	194305	.	C	CGG	1602.78	.	AB=0.0;AO=58;DP=59;QA=1889;QR=0;RO=0;TYPE=ins	GT:DP:RO:QR:AO:QA:GL	1/1:59:0:0:58:1889:-169.924,-17.4597,0.0
Chromosome	2738274	.	A	C	511.15	.	AB=0.0;AO=18;DP=19;QA=633;QR=35;RO=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:19:1:35:18:633:-53.7923,-2.22094,0.0
Chromosome	3750185	.	CGAC	GGTG	1102.73	.	AB=0.0;AO=36;DP=36;QA=1255;QR=0;RO=0;TYPE=complex	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1255:-113.24,-10.8371,0.0