diff test-data/freebayes_vcf_to_gff_output.gff @ 5:b321e0517be3 draft

Uploaded
author ben-warren
date Thu, 22 May 2014 20:30:19 -0400
parents
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes_vcf_to_gff_output.gff	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,449 @@
+#gff-version 3
+Chr1	SAMTOOLS	SNP	106	106	17.1701	.	.	ID=Chr1:SNP:106;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	200	200	17.1701	.	.	ID=Chr1:SNP:200;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	217	217	4.77465	.	.	ID=Chr1:SNP:217;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	249	249	4.77465	.	.	ID=Chr1:SNP:249;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	586	586	17.1701	.	.	ID=Chr1:SNP:586;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	669	669	4.77465	.	.	ID=Chr1:SNP:669;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	682	682	4.77465	.	.	ID=Chr1:SNP:682;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	1007	1007	17.1701	.	.	ID=Chr1:SNP:1007;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1012	1012	17.1701	.	.	ID=Chr1:SNP:1012;Variant_seq=AGA;Reference_seq=TGT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1056	1056	17.1701	.	.	ID=Chr1:SNP:1056;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1067	1067	17.1701	.	.	ID=Chr1:SNP:1067;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1257	1257	17.1701	.	.	ID=Chr1:SNP:1257;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1305	1305	17.1701	.	.	ID=Chr1:SNP:1305;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1319	1319	17.1701	.	.	ID=Chr1:SNP:1319;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1330	1330	17.1701	.	.	ID=Chr1:SNP:1330;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1441	1441	17.1701	.	.	ID=Chr1:SNP:1441;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1451	1451	17.1701	.	.	ID=Chr1:SNP:1451;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1460	1460	17.1701	.	.	ID=Chr1:SNP:1460;Variant_seq=ATCTC;Reference_seq=CTCTG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1480	1480	17.1701	.	.	ID=Chr1:SNP:1480;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1525	1525	17.1701	.	.	ID=Chr1:SNP:1525;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	1670	1670	4.77465	.	.	ID=Chr1:SNP:1670;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	1673	1673	4.77465	.	.	ID=Chr1:SNP:1673;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	1700	1700	4.77465	.	.	ID=Chr1:SNP:1700;Variant_seq=TG;Reference_seq=GC;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	1711	1711	4.77465	.	.	ID=Chr1:SNP:1711;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	2117	2117	17.1701	.	.	ID=Chr1:SNP:2117;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	2154	2154	17.1701	.	.	ID=Chr1:SNP:2154;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	2485	2485	17.1701	.	.	ID=Chr1:SNP:2485;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	2490	2490	17.1701	.	.	ID=Chr1:SNP:2490;Variant_seq=CAC;Reference_seq=AAA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	2906	2906	17.1701	.	.	ID=Chr1:SNP:2906;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	2925	2925	17.1701	.	.	ID=Chr1:SNP:2925;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	3371	3371	17.1701	.	.	ID=Chr1:SNP:3371;Variant_seq=GCCTA;Reference_seq=CCCTT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	3389	3389	17.1701	.	.	ID=Chr1:SNP:3389;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	3431	3431	17.1701	.	.	ID=Chr1:SNP:3431;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	3464	3464	17.1701	.	.	ID=Chr1:SNP:3464;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	3746	3746	46.0861	.	.	ID=Chr1:SNP:3746;Variant_seq=CT;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	3766	3766	4.77465	.	.	ID=Chr1:SNP:3766;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	3790	3790	4.77465	.	.	ID=Chr1:SNP:3790;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	3855	3855	17.1701	.	.	ID=Chr1:SNP:3855;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	5718	5718	17.1701	.	.	ID=Chr1:SNP:5718;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	5754	5754	17.1701	.	.	ID=Chr1:SNP:5754;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	5782	5782	17.1701	.	.	ID=Chr1:SNP:5782;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	5792	5792	17.1701	.	.	ID=Chr1:SNP:5792;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6194	6194	17.1701	.	.	ID=Chr1:SNP:6194;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6212	6212	17.1701	.	.	ID=Chr1:SNP:6212;Variant_seq=A;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6265	6265	17.1701	.	.	ID=Chr1:SNP:6265;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6482	6482	17.1701	.	.	ID=Chr1:SNP:6482;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6515	6515	17.1701	.	.	ID=Chr1:SNP:6515;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6520	6520	17.1701	.	.	ID=Chr1:SNP:6520;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6534	6534	17.1701	.	.	ID=Chr1:SNP:6534;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6602	6602	17.1701	.	.	ID=Chr1:SNP:6602;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	6853	6853	17.1701	.	.	ID=Chr1:SNP:6853;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7015	7015	17.1701	.	.	ID=Chr1:SNP:7015;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7406	7406	17.1701	.	.	ID=Chr1:SNP:7406;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7422	7422	17.1701	.	.	ID=Chr1:SNP:7422;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7452	7452	17.1701	.	.	ID=Chr1:SNP:7452;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7460	7460	17.1701	.	.	ID=Chr1:SNP:7460;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7476	7476	17.1701	.	.	ID=Chr1:SNP:7476;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7843	7843	17.1701	.	.	ID=Chr1:SNP:7843;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	7906	7906	17.1701	.	.	ID=Chr1:SNP:7906;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8214	8214	17.1701	.	.	ID=Chr1:SNP:8214;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8262	8262	17.1701	.	.	ID=Chr1:SNP:8262;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8279	8279	4.77465	.	.	ID=Chr1:SNP:8279;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	8285	8285	4.77465	.	.	ID=Chr1:SNP:8285;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	8288	8288	4.77465	.	.	ID=Chr1:SNP:8288;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	8298	8298	4.77465	.	.	ID=Chr1:SNP:8298;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	8305	8305	4.77465	.	.	ID=Chr1:SNP:8305;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	8329	8329	17.1701	.	.	ID=Chr1:SNP:8329;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8509	8509	17.1701	.	.	ID=Chr1:SNP:8509;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8547	8547	17.1701	.	.	ID=Chr1:SNP:8547;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8633	8633	17.1701	.	.	ID=Chr1:SNP:8633;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8657	8657	17.1701	.	.	ID=Chr1:SNP:8657;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8894	8894	17.1701	.	.	ID=Chr1:SNP:8894;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8958	8958	17.1701	.	.	ID=Chr1:SNP:8958;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	8968	8968	17.1701	.	.	ID=Chr1:SNP:8968;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	9070	9070	17.1701	.	.	ID=Chr1:SNP:9070;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	9100	9100	17.1701	.	.	ID=Chr1:SNP:9100;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	9488	9488	17.1701	.	.	ID=Chr1:SNP:9488;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	9514	9514	4.77465	.	.	ID=Chr1:SNP:9514;Variant_seq=CTTG;Reference_seq=GTTT;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	9532	9532	4.77465	.	.	ID=Chr1:SNP:9532;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	10064	10064	17.1701	.	.	ID=Chr1:SNP:10064;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	10072	10072	17.1701	.	.	ID=Chr1:SNP:10072;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	10082	10082	17.1701	.	.	ID=Chr1:SNP:10082;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	10099	10099	17.1701	.	.	ID=Chr1:SNP:10099;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	10499	10499	17.1701	.	.	ID=Chr1:SNP:10499;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	11126	11126	4.77465	.	.	ID=Chr1:SNP:11126;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	11134	11134	4.77465	.	.	ID=Chr1:SNP:11134;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	11141	11141	4.77465	.	.	ID=Chr1:SNP:11141;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	11159	11159	4.77465	.	.	ID=Chr1:SNP:11159;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	11169	11169	4.77465	.	.	ID=Chr1:SNP:11169;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	11208	11208	17.1701	.	.	ID=Chr1:SNP:11208;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	11418	11418	17.1701	.	.	ID=Chr1:SNP:11418;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	11547	11547	4.77465	.	.	ID=Chr1:SNP:11547;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	11567	11567	4.77465	.	.	ID=Chr1:SNP:11567;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	11582	11582	17.1701	.	.	ID=Chr1:SNP:11582;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	13312	13312	17.1701	.	.	ID=Chr1:SNP:13312;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	13336	13336	17.1701	.	.	ID=Chr1:SNP:13336;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	13352	13352	17.1701	.	.	ID=Chr1:SNP:13352;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	13652	13652	17.1701	.	.	ID=Chr1:SNP:13652;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	13666	13666	17.1701	.	.	ID=Chr1:SNP:13666;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	13728	13728	4.77465	.	.	ID=Chr1:SNP:13728;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	14087	14087	4.77465	.	.	ID=Chr1:SNP:14087;Variant_seq=GTGAGC;Reference_seq=ATGAAA;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	14103	14103	4.77465	.	.	ID=Chr1:SNP:14103;Variant_seq=GGC;Reference_seq=AGT;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	14119	14119	4.77465	.	.	ID=Chr1:SNP:14119;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	14126	14126	4.77465	.	.	ID=Chr1:SNP:14126;Variant_seq=G;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	14131	14131	2.50735	.	.	ID=Chr1:SNP:14131;Variant_seq=TGGGTT;Reference_seq=GGAGTG;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	14141	14141	2.50735	.	.	ID=Chr1:SNP:14141;Variant_seq=CCC;Reference_seq=TCA;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	14159	14159	2.50735	.	.	ID=Chr1:SNP:14159;Variant_seq=A;Reference_seq=G;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	14165	14165	7.01833	.	.	ID=Chr1:SNP:14165;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HOM_mut 
+Chr1	SAMTOOLS	SNP	14167	14167	2.50735	.	.	ID=Chr1:SNP:14167;Variant_seq=T;Reference_seq=A;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	14182	14182	4.77465	.	.	ID=Chr1:SNP:14182;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	14201	14201	17.1701	.	.	ID=Chr1:SNP:14201;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14210	14210	17.1701	.	.	ID=Chr1:SNP:14210;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14230	14230	17.1701	.	.	ID=Chr1:SNP:14230;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14240	14240	17.1701	.	.	ID=Chr1:SNP:14240;Variant_seq=T;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14247	14247	17.1701	.	.	ID=Chr1:SNP:14247;Variant_seq=A;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14256	14256	17.1701	.	.	ID=Chr1:SNP:14256;Variant_seq=G;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14262	14262	17.1701	.	.	ID=Chr1:SNP:14262;Variant_seq=CC;Reference_seq=TT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14292	14292	17.1701	.	.	ID=Chr1:SNP:14292;Variant_seq=CCTA;Reference_seq=TCTG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14306	14306	17.1701	.	.	ID=Chr1:SNP:14306;Variant_seq=TT;Reference_seq=AC;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14312	14312	17.1701	.	.	ID=Chr1:SNP:14312;Variant_seq=TA;Reference_seq=CG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14320	14320	17.1701	.	.	ID=Chr1:SNP:14320;Variant_seq=TCCCTA;Reference_seq=TCTTT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14327	14327	17.1701	.	.	ID=Chr1:SNP:14327;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14595	14595	17.1701	.	.	ID=Chr1:SNP:14595;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14624	14624	17.1701	.	.	ID=Chr1:SNP:14624;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14629	14629	17.1701	.	.	ID=Chr1:SNP:14629;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	14724	14724	17.1701	.	.	ID=Chr1:SNP:14724;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	15170	15170	17.1701	.	.	ID=Chr1:SNP:15170;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	15183	15183	4.77465	.	.	ID=Chr1:SNP:15183;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	15199	15199	17.1701	.	.	ID=Chr1:SNP:15199;Variant_seq=AAT;Reference_seq=CAA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	15209	15209	17.1701	.	.	ID=Chr1:SNP:15209;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	15599	15599	17.1701	.	.	ID=Chr1:SNP:15599;Variant_seq=GGC;Reference_seq=TGG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	15624	15624	4.77465	.	.	ID=Chr1:SNP:15624;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	15625	15625	4.77465	.	.	ID=Chr1:SNP:15625;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	15670	15670	4.77465	.	.	ID=Chr1:SNP:15670;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	15685	15685	17.1701	.	.	ID=Chr1:SNP:15685;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	15696	15696	17.1701	.	.	ID=Chr1:SNP:15696;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	15981	15981	17.1701	.	.	ID=Chr1:SNP:15981;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	16021	16021	17.1701	.	.	ID=Chr1:SNP:16021;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	16050	16050	17.1701	.	.	ID=Chr1:SNP:16050;Variant_seq=ATGGC;Reference_seq=CTGGG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	16059	16059	4.77465	.	.	ID=Chr1:SNP:16059;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	16085	16085	17.1701	.	.	ID=Chr1:SNP:16085;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	16287	16287	17.1701	.	.	ID=Chr1:SNP:16287;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	16502	16502	17.1701	.	.	ID=Chr1:SNP:16502;Variant_seq=CCT;Reference_seq=GCA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	16512	16512	17.1701	.	.	ID=Chr1:SNP:16512;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	16519	16519	17.1701	.	.	ID=Chr1:SNP:16519;Variant_seq=GGTGG;Reference_seq=TGTGT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	17672	17672	17.1701	.	.	ID=Chr1:SNP:17672;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	17738	17738	17.1701	.	.	ID=Chr1:SNP:17738;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	17849	17849	17.1701	.	.	ID=Chr1:SNP:17849;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	17873	17873	17.1701	.	.	ID=Chr1:SNP:17873;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	17878	17878	17.1701	.	.	ID=Chr1:SNP:17878;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18083	18083	17.1701	.	.	ID=Chr1:SNP:18083;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18090	18090	17.1701	.	.	ID=Chr1:SNP:18090;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18099	18099	17.1701	.	.	ID=Chr1:SNP:18099;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18205	18205	17.1701	.	.	ID=Chr1:SNP:18205;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18275	18275	17.1701	.	.	ID=Chr1:SNP:18275;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18285	18285	17.1701	.	.	ID=Chr1:SNP:18285;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18320	18320	17.1701	.	.	ID=Chr1:SNP:18320;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18370	18370	17.1701	.	.	ID=Chr1:SNP:18370;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	18416	18416	17.1701	.	.	ID=Chr1:SNP:18416;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	20586	20586	4.77465	.	.	ID=Chr1:SNP:20586;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	20604	20604	4.77465	.	.	ID=Chr1:SNP:20604;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	20625	20625	2.50735	.	.	ID=Chr1:SNP:20625;Variant_seq=T;Reference_seq=G;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	20692	20692	4.77465	.	.	ID=Chr1:SNP:20692;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	20702	20702	4.77465	.	.	ID=Chr1:SNP:20702;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	20720	20720	17.1701	.	.	ID=Chr1:SNP:20720;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	20891	20891	17.1701	.	.	ID=Chr1:SNP:20891;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	20922	20922	17.1701	.	.	ID=Chr1:SNP:20922;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	20967	20967	17.1701	.	.	ID=Chr1:SNP:20967;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	20998	20998	17.1701	.	.	ID=Chr1:SNP:20998;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21007	21007	17.1701	.	.	ID=Chr1:SNP:21007;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21042	21042	4.77465	.	.	ID=Chr1:SNP:21042;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	21055	21055	4.77465	.	.	ID=Chr1:SNP:21055;Variant_seq=A;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	21080	21080	4.77465	.	.	ID=Chr1:SNP:21080;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	21165	21165	4.77465	.	.	ID=Chr1:SNP:21165;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	21189	21189	4.77465	.	.	ID=Chr1:SNP:21189;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	21202	21202	20.1741	.	.	ID=Chr1:SNP:21202;Variant_seq=CCCA,TCCT;Reference_seq=ACCT;Total_reads=2;Zygosity=2:NA 
+Chr1	SAMTOOLS	SNP	21322	21322	17.1701	.	.	ID=Chr1:SNP:21322;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21342	21342	17.1701	.	.	ID=Chr1:SNP:21342;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21359	21359	17.1701	.	.	ID=Chr1:SNP:21359;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21584	21584	17.1701	.	.	ID=Chr1:SNP:21584;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21615	21615	17.1701	.	.	ID=Chr1:SNP:21615;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21821	21821	17.1701	.	.	ID=Chr1:SNP:21821;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21936	21936	17.1701	.	.	ID=Chr1:SNP:21936;Variant_seq=AGA;Reference_seq=TGT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	21955	21955	17.1701	.	.	ID=Chr1:SNP:21955;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22337	22337	17.1701	.	.	ID=Chr1:SNP:22337;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22345	22345	17.1701	.	.	ID=Chr1:SNP:22345;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22415	22415	17.1701	.	.	ID=Chr1:SNP:22415;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22429	22429	17.1701	.	.	ID=Chr1:SNP:22429;Variant_seq=CTTT;Reference_seq=ATTG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22520	22520	17.1701	.	.	ID=Chr1:SNP:22520;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22539	22539	17.1701	.	.	ID=Chr1:SNP:22539;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22742	22742	17.1701	.	.	ID=Chr1:SNP:22742;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22801	22801	17.1701	.	.	ID=Chr1:SNP:22801;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22888	22888	17.1701	.	.	ID=Chr1:SNP:22888;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	22919	22919	17.1701	.	.	ID=Chr1:SNP:22919;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23346	23346	17.1701	.	.	ID=Chr1:SNP:23346;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23360	23360	17.1701	.	.	ID=Chr1:SNP:23360;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23390	23390	17.1701	.	.	ID=Chr1:SNP:23390;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23432	23432	17.1701	.	.	ID=Chr1:SNP:23432;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23687	23687	17.1701	.	.	ID=Chr1:SNP:23687;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23716	23716	17.1701	.	.	ID=Chr1:SNP:23716;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23745	23745	17.1701	.	.	ID=Chr1:SNP:23745;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23812	23812	17.1701	.	.	ID=Chr1:SNP:23812;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23829	23829	17.1701	.	.	ID=Chr1:SNP:23829;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23959	23959	17.1701	.	.	ID=Chr1:SNP:23959;Variant_seq=AG;Reference_seq=TC;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	23989	23989	17.1701	.	.	ID=Chr1:SNP:23989;Variant_seq=CTCA;Reference_seq=ATCT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	24095	24095	17.1701	.	.	ID=Chr1:SNP:24095;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	24350	24350	17.1701	.	.	ID=Chr1:SNP:24350;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	24377	24377	17.1701	.	.	ID=Chr1:SNP:24377;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	24395	24395	4.77465	.	.	ID=Chr1:SNP:24395;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	24413	24413	4.77465	.	.	ID=Chr1:SNP:24413;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	24416	24416	4.77465	.	.	ID=Chr1:SNP:24416;Variant_seq=TAGA;Reference_seq=GAGT;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	24467	24467	17.1701	.	.	ID=Chr1:SNP:24467;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	24477	24477	17.1701	.	.	ID=Chr1:SNP:24477;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	24846	24846	17.1701	.	.	ID=Chr1:SNP:24846;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	24889	24889	4.77465	.	.	ID=Chr1:SNP:24889;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	24923	24923	4.77465	.	.	ID=Chr1:SNP:24923;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	24964	24964	17.1701	.	.	ID=Chr1:SNP:24964;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	25174	25174	17.1701	.	.	ID=Chr1:SNP:25174;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	25301	25301	4.77465	.	.	ID=Chr1:SNP:25301;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	25320	25320	4.77465	.	.	ID=Chr1:SNP:25320;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	25345	25345	4.77465	.	.	ID=Chr1:SNP:25345;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	25355	25355	17.1701	.	.	ID=Chr1:SNP:25355;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	25550	25550	4.77465	.	.	ID=Chr1:SNP:25550;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	25580	25580	2.50735	.	.	ID=Chr1:SNP:25580;Variant_seq=T;Reference_seq=A;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	25584	25584	2.50735	.	.	ID=Chr1:SNP:25584;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	25626	25626	2.50735	.	.	ID=Chr1:SNP:25626;Variant_seq=TCAG;Reference_seq=GCAC;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	25644	25644	2.50735	.	.	ID=Chr1:SNP:25644;Variant_seq=C;Reference_seq=A;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	25687	25687	4.77465	.	.	ID=Chr1:SNP:25687;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	25696	25696	20.1741	.	.	ID=Chr1:SNP:25696;Variant_seq=GCTCT,GCTCA;Reference_seq=ACTCA;Total_reads=2;Zygosity=2:NA 
+Chr1	SAMTOOLS	SNP	25944	25944	17.1701	.	.	ID=Chr1:SNP:25944;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	25972	25972	4.77465	.	.	ID=Chr1:SNP:25972;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	25981	25981	2.50735	.	.	ID=Chr1:SNP:25981;Variant_seq=T;Reference_seq=G;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	25983	25983	2.50735	.	.	ID=Chr1:SNP:25983;Variant_seq=TT;Reference_seq=AA;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	26001	26001	1.76687	.	.	ID=Chr1:SNP:26001;Variant_seq=C;Reference_seq=G;Total_reads=4;Zygosity=4:HET 
+Chr1	SAMTOOLS	SNP	26364	26364	17.1701	.	.	ID=Chr1:SNP:26364;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	26420	26420	17.1701	.	.	ID=Chr1:SNP:26420;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	27175	27175	17.1701	.	.	ID=Chr1:SNP:27175;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	27431	27431	17.1701	.	.	ID=Chr1:SNP:27431;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	27472	27472	17.1701	.	.	ID=Chr1:SNP:27472;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	27556	27556	46.0861	.	.	ID=Chr1:SNP:27556;Variant_seq=AT;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	27610	27610	17.1701	.	.	ID=Chr1:SNP:27610;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	27909	27909	17.1701	.	.	ID=Chr1:SNP:27909;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	28614	28614	17.1701	.	.	ID=Chr1:SNP:28614;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	28993	28993	4.77465	.	.	ID=Chr1:SNP:28993;Variant_seq=GGGC;Reference_seq=TGGG;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	29022	29022	2.50735	.	.	ID=Chr1:SNP:29022;Variant_seq=A;Reference_seq=T;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	29026	29026	2.50735	.	.	ID=Chr1:SNP:29026;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	29032	29032	2.50735	.	.	ID=Chr1:SNP:29032;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	29080	29080	17.1701	.	.	ID=Chr1:SNP:29080;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	29218	29218	17.1701	.	.	ID=Chr1:SNP:29218;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	29342	29342	17.1701	.	.	ID=Chr1:SNP:29342;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	29463	29463	17.1701	.	.	ID=Chr1:SNP:29463;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	29516	29516	4.77465	.	.	ID=Chr1:SNP:29516;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	29528	29528	4.77465	.	.	ID=Chr1:SNP:29528;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	29575	29575	17.1701	.	.	ID=Chr1:SNP:29575;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	29580	29580	17.1701	.	.	ID=Chr1:SNP:29580;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	30681	30681	17.1701	.	.	ID=Chr1:SNP:30681;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	30735	30735	17.1701	.	.	ID=Chr1:SNP:30735;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	30766	30766	17.1701	.	.	ID=Chr1:SNP:30766;Variant_seq=GTATA;Reference_seq=CTATT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	31019	31019	17.1701	.	.	ID=Chr1:SNP:31019;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	31054	31054	4.77465	.	.	ID=Chr1:SNP:31054;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	31101	31101	17.1701	.	.	ID=Chr1:SNP:31101;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	31400	31400	17.1701	.	.	ID=Chr1:SNP:31400;Variant_seq=CG;Reference_seq=GT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	31422	31422	17.1701	.	.	ID=Chr1:SNP:31422;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	32027	32027	17.1701	.	.	ID=Chr1:SNP:32027;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	32060	32060	17.1701	.	.	ID=Chr1:SNP:32060;Variant_seq=T;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	32166	32166	17.1701	.	.	ID=Chr1:SNP:32166;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	32226	32226	17.1701	.	.	ID=Chr1:SNP:32226;Variant_seq=CC;Reference_seq=AA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	32480	32480	17.1701	.	.	ID=Chr1:SNP:32480;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	32491	32491	17.1701	.	.	ID=Chr1:SNP:32491;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	32651	32651	4.77465	.	.	ID=Chr1:SNP:32651;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	32934	32934	17.1701	.	.	ID=Chr1:SNP:32934;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33054	33054	17.1701	.	.	ID=Chr1:SNP:33054;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33109	33109	17.1701	.	.	ID=Chr1:SNP:33109;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33143	33143	17.1701	.	.	ID=Chr1:SNP:33143;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33245	33245	17.1701	.	.	ID=Chr1:SNP:33245;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33274	33274	17.1701	.	.	ID=Chr1:SNP:33274;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33377	33377	17.1701	.	.	ID=Chr1:SNP:33377;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33392	33392	17.1701	.	.	ID=Chr1:SNP:33392;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33417	33417	17.1701	.	.	ID=Chr1:SNP:33417;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	33713	33713	4.77465	.	.	ID=Chr1:SNP:33713;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	33746	33746	17.1701	.	.	ID=Chr1:SNP:33746;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	35247	35247	17.1701	.	.	ID=Chr1:SNP:35247;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	35679	35679	17.1701	.	.	ID=Chr1:SNP:35679;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	36145	36145	17.1701	.	.	ID=Chr1:SNP:36145;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	36591	36591	17.1701	.	.	ID=Chr1:SNP:36591;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	37260	37260	17.1701	.	.	ID=Chr1:SNP:37260;Variant_seq=CA;Reference_seq=AT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	37270	37270	17.1701	.	.	ID=Chr1:SNP:37270;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	37283	37283	4.77465	.	.	ID=Chr1:SNP:37283;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	37284	37284	4.77465	.	.	ID=Chr1:SNP:37284;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	37295	37295	4.77465	.	.	ID=Chr1:SNP:37295;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	37321	37321	17.1701	.	.	ID=Chr1:SNP:37321;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	37610	37610	17.1701	.	.	ID=Chr1:SNP:37610;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	37673	37673	17.1701	.	.	ID=Chr1:SNP:37673;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	38268	38268	17.1701	.	.	ID=Chr1:SNP:38268;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	38656	38656	17.1701	.	.	ID=Chr1:SNP:38656;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	39013	39013	17.1701	.	.	ID=Chr1:SNP:39013;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	39023	39023	17.1701	.	.	ID=Chr1:SNP:39023;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	39460	39460	4.77465	.	.	ID=Chr1:SNP:39460;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	39480	39480	4.77465	.	.	ID=Chr1:SNP:39480;Variant_seq=TC;Reference_seq=GA;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	39501	39501	4.77465	.	.	ID=Chr1:SNP:39501;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	39508	39508	4.77465	.	.	ID=Chr1:SNP:39508;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	41835	41835	17.1701	.	.	ID=Chr1:SNP:41835;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	41885	41885	17.1701	.	.	ID=Chr1:SNP:41885;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	42284	42284	17.1701	.	.	ID=Chr1:SNP:42284;Variant_seq=TGTTG;Reference_seq=AGTTT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	42628	42628	17.1701	.	.	ID=Chr1:SNP:42628;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	42637	42637	17.1701	.	.	ID=Chr1:SNP:42637;Variant_seq=CTTCG;Reference_seq=ATTCC;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	42652	42652	17.1701	.	.	ID=Chr1:SNP:42652;Variant_seq=ATTGA;Reference_seq=TTTGT;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	43145	43145	17.1701	.	.	ID=Chr1:SNP:43145;Variant_seq=CC;Reference_seq=GG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	43164	43164	17.1701	.	.	ID=Chr1:SNP:43164;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	43173	43173	17.1701	.	.	ID=Chr1:SNP:43173;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	43219	43219	17.1701	.	.	ID=Chr1:SNP:43219;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	43437	43437	17.1701	.	.	ID=Chr1:SNP:43437;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	44980	44980	17.1701	.	.	ID=Chr1:SNP:44980;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45144	45144	17.1701	.	.	ID=Chr1:SNP:45144;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45166	45166	17.1701	.	.	ID=Chr1:SNP:45166;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45311	45311	17.1701	.	.	ID=Chr1:SNP:45311;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45333	45333	17.1701	.	.	ID=Chr1:SNP:45333;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45385	45385	17.1701	.	.	ID=Chr1:SNP:45385;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45419	45419	17.1701	.	.	ID=Chr1:SNP:45419;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45427	45427	17.1701	.	.	ID=Chr1:SNP:45427;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	45663	45663	4.77465	.	.	ID=Chr1:SNP:45663;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	45685	45685	4.77465	.	.	ID=Chr1:SNP:45685;Variant_seq=CT;Reference_seq=AG;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	46052	46052	17.1701	.	.	ID=Chr1:SNP:46052;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	46117	46117	17.1701	.	.	ID=Chr1:SNP:46117;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	46251	46251	17.1701	.	.	ID=Chr1:SNP:46251;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	46261	46261	17.1701	.	.	ID=Chr1:SNP:46261;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	47385	47385	17.1701	.	.	ID=Chr1:SNP:47385;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	47414	47414	17.1701	.	.	ID=Chr1:SNP:47414;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	48446	48446	4.77465	.	.	ID=Chr1:SNP:48446;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	48526	48526	4.77465	.	.	ID=Chr1:SNP:48526;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	48789	48789	4.77465	.	.	ID=Chr1:SNP:48789;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	48796	48796	4.77465	.	.	ID=Chr1:SNP:48796;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	48811	48811	4.77465	.	.	ID=Chr1:SNP:48811;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	48831	48831	4.77465	.	.	ID=Chr1:SNP:48831;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	48838	48838	4.77465	.	.	ID=Chr1:SNP:48838;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	48852	48852	2.50735	.	.	ID=Chr1:SNP:48852;Variant_seq=T;Reference_seq=A;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	48907	48907	17.1701	.	.	ID=Chr1:SNP:48907;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	48936	48936	17.1701	.	.	ID=Chr1:SNP:48936;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	49044	49044	17.1701	.	.	ID=Chr1:SNP:49044;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	49059	49059	2.50735	.	.	ID=Chr1:SNP:49059;Variant_seq=C;Reference_seq=A;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	49086	49086	2.50735	.	.	ID=Chr1:SNP:49086;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	49088	49088	2.50735	.	.	ID=Chr1:SNP:49088;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	49091	49091	2.50735	.	.	ID=Chr1:SNP:49091;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	49099	49099	2.50735	.	.	ID=Chr1:SNP:49099;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	49124	49124	2.50735	.	.	ID=Chr1:SNP:49124;Variant_seq=TAAA;Reference_seq=AAAC;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	49134	49134	2.50735	.	.	ID=Chr1:SNP:49134;Variant_seq=A;Reference_seq=C;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	49493	49493	17.1701	.	.	ID=Chr1:SNP:49493;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	49543	49543	17.1701	.	.	ID=Chr1:SNP:49543;Variant_seq=GGCAT;Reference_seq=TGCAA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	49553	49553	17.1701	.	.	ID=Chr1:SNP:49553;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	49583	49583	17.1701	.	.	ID=Chr1:SNP:49583;Variant_seq=C;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	50222	50222	17.1701	.	.	ID=Chr1:SNP:50222;Variant_seq=CCCACTC;Reference_seq=ACAAAGA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	50557	50557	4.77465	.	.	ID=Chr1:SNP:50557;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	50574	50574	4.77465	.	.	ID=Chr1:SNP:50574;Variant_seq=C;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	50603	50603	17.1701	.	.	ID=Chr1:SNP:50603;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	50790	50790	17.1701	.	.	ID=Chr1:SNP:50790;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	50828	50828	17.1701	.	.	ID=Chr1:SNP:50828;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	50843	50843	17.1701	.	.	ID=Chr1:SNP:50843;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	50958	50958	17.1701	.	.	ID=Chr1:SNP:50958;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	51330	51330	4.77465	.	.	ID=Chr1:SNP:51330;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	51606	51606	17.1701	.	.	ID=Chr1:SNP:51606;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	51681	51681	17.1701	.	.	ID=Chr1:SNP:51681;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	51984	51984	17.1701	.	.	ID=Chr1:SNP:51984;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	51996	51996	17.1701	.	.	ID=Chr1:SNP:51996;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	52061	52061	17.1701	.	.	ID=Chr1:SNP:52061;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	53145	53145	17.1701	.	.	ID=Chr1:SNP:53145;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	53423	53423	17.1701	.	.	ID=Chr1:SNP:53423;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	53442	53442	17.1701	.	.	ID=Chr1:SNP:53442;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	54071	54071	17.1701	.	.	ID=Chr1:SNP:54071;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	54472	54472	17.1701	.	.	ID=Chr1:SNP:54472;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	54525	54525	17.1701	.	.	ID=Chr1:SNP:54525;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	54562	54562	17.1701	.	.	ID=Chr1:SNP:54562;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	55358	55358	17.1701	.	.	ID=Chr1:SNP:55358;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	55372	55372	17.1701	.	.	ID=Chr1:SNP:55372;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	55415	55415	17.1701	.	.	ID=Chr1:SNP:55415;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	55460	55460	17.1701	.	.	ID=Chr1:SNP:55460;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	55491	55491	17.1701	.	.	ID=Chr1:SNP:55491;Variant_seq=CC;Reference_seq=AA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	55917	55917	17.1701	.	.	ID=Chr1:SNP:55917;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56372	56372	4.77465	.	.	ID=Chr1:SNP:56372;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	56383	56383	2.50735	.	.	ID=Chr1:SNP:56383;Variant_seq=T;Reference_seq=G;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	56399	56399	4.77465	.	.	ID=Chr1:SNP:56399;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	56430	56430	4.77465	.	.	ID=Chr1:SNP:56430;Variant_seq=C;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	56448	56448	4.77465	.	.	ID=Chr1:SNP:56448;Variant_seq=G;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	56477	56477	17.1701	.	.	ID=Chr1:SNP:56477;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56586	56586	17.1701	.	.	ID=Chr1:SNP:56586;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56642	56642	17.1701	.	.	ID=Chr1:SNP:56642;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56672	56672	46.0861	.	.	ID=Chr1:SNP:56672;Variant_seq=TA;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56708	56708	17.1701	.	.	ID=Chr1:SNP:56708;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56728	56728	17.1701	.	.	ID=Chr1:SNP:56728;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56743	56743	17.1701	.	.	ID=Chr1:SNP:56743;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	56750	56750	1.76687	.	.	ID=Chr1:SNP:56750;Variant_seq=C;Reference_seq=G;Total_reads=4;Zygosity=4:HET 
+Chr1	SAMTOOLS	SNP	56756	56756	1.76687	.	.	ID=Chr1:SNP:56756;Variant_seq=T;Reference_seq=A;Total_reads=4;Zygosity=4:HET 
+Chr1	SAMTOOLS	SNP	56769	56769	1.76687	.	.	ID=Chr1:SNP:56769;Variant_seq=T;Reference_seq=A;Total_reads=4;Zygosity=4:HET 
+Chr1	SAMTOOLS	SNP	56792	56792	1.76687	.	.	ID=Chr1:SNP:56792;Variant_seq=T;Reference_seq=A;Total_reads=4;Zygosity=4:HET 
+Chr1	SAMTOOLS	SNP	56800	56800	1.76687	.	.	ID=Chr1:SNP:56800;Variant_seq=T;Reference_seq=A;Total_reads=4;Zygosity=4:HET 
+Chr1	SAMTOOLS	SNP	56803	56803	1.76687	.	.	ID=Chr1:SNP:56803;Variant_seq=G;Reference_seq=C;Total_reads=4;Zygosity=4:HET 
+Chr1	SAMTOOLS	SNP	56822	56822	2.50735	.	.	ID=Chr1:SNP:56822;Variant_seq=T;Reference_seq=A;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	57075	57075	4.77465	.	.	ID=Chr1:SNP:57075;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	57129	57129	4.77465	.	.	ID=Chr1:SNP:57129;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	57130	57130	4.77465	.	.	ID=Chr1:SNP:57130;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	57164	57164	17.1701	.	.	ID=Chr1:SNP:57164;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	57166	57166	17.1701	.	.	ID=Chr1:SNP:57166;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	57533	57533	17.1701	.	.	ID=Chr1:SNP:57533;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	57543	57543	17.1701	.	.	ID=Chr1:SNP:57543;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	57561	57561	17.1701	.	.	ID=Chr1:SNP:57561;Variant_seq=ATCGC;Reference_seq=TTCGA;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	57885	57885	17.1701	.	.	ID=Chr1:SNP:57885;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	57929	57929	17.1701	.	.	ID=Chr1:SNP:57929;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58372	58372	17.1701	.	.	ID=Chr1:SNP:58372;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58383	58383	17.1701	.	.	ID=Chr1:SNP:58383;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58391	58391	17.1701	.	.	ID=Chr1:SNP:58391;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58399	58399	17.1701	.	.	ID=Chr1:SNP:58399;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58807	58807	17.1701	.	.	ID=Chr1:SNP:58807;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58825	58825	17.1701	.	.	ID=Chr1:SNP:58825;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58844	58844	17.1701	.	.	ID=Chr1:SNP:58844;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	58862	58862	4.77465	.	.	ID=Chr1:SNP:58862;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	59508	59508	17.1701	.	.	ID=Chr1:SNP:59508;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	59524	59524	17.1701	.	.	ID=Chr1:SNP:59524;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	59546	59546	17.1701	.	.	ID=Chr1:SNP:59546;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	59554	59554	46.0861	.	.	ID=Chr1:SNP:59554;Variant_seq=CG;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61378	61378	17.1701	.	.	ID=Chr1:SNP:61378;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61387	61387	17.1701	.	.	ID=Chr1:SNP:61387;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61599	61599	17.1701	.	.	ID=Chr1:SNP:61599;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61652	61652	17.1701	.	.	ID=Chr1:SNP:61652;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61882	61882	17.1701	.	.	ID=Chr1:SNP:61882;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61904	61904	17.1701	.	.	ID=Chr1:SNP:61904;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61913	61913	17.1701	.	.	ID=Chr1:SNP:61913;Variant_seq=TGC;Reference_seq=AGG;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	61957	61957	17.1701	.	.	ID=Chr1:SNP:61957;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62010	62010	17.1701	.	.	ID=Chr1:SNP:62010;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62056	62056	4.77465	.	.	ID=Chr1:SNP:62056;Variant_seq=A;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	62168	62168	17.1701	.	.	ID=Chr1:SNP:62168;Variant_seq=GCGCG;Reference_seq=CCGCC;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62290	62290	17.1701	.	.	ID=Chr1:SNP:62290;Variant_seq=A;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62446	62446	2.50735	.	.	ID=Chr1:SNP:62446;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	62447	62447	2.50735	.	.	ID=Chr1:SNP:62447;Variant_seq=ATAC;Reference_seq=CTAG;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	62462	62462	2.50735	.	.	ID=Chr1:SNP:62462;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	62478	62478	2.50735	.	.	ID=Chr1:SNP:62478;Variant_seq=G;Reference_seq=C;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	62514	62514	4.77465	.	.	ID=Chr1:SNP:62514;Variant_seq=T;Reference_seq=G;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	62598	62598	17.1701	.	.	ID=Chr1:SNP:62598;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62634	62634	4.77465	.	.	ID=Chr1:SNP:62634;Variant_seq=G;Reference_seq=T;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	62658	62658	2.50735	.	.	ID=Chr1:SNP:62658;Variant_seq=G;Reference_seq=T;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	62665	62665	2.50735	.	.	ID=Chr1:SNP:62665;Variant_seq=C;Reference_seq=G;Total_reads=3;Zygosity=3:HET 
+Chr1	SAMTOOLS	SNP	62686	62686	4.77465	.	.	ID=Chr1:SNP:62686;Variant_seq=T;Reference_seq=A;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	62697	62697	4.77465	.	.	ID=Chr1:SNP:62697;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET 
+Chr1	SAMTOOLS	SNP	62758	62758	17.1701	.	.	ID=Chr1:SNP:62758;Variant_seq=T;Reference_seq=G;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62769	62769	17.1701	.	.	ID=Chr1:SNP:62769;Variant_seq=C;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62841	62841	17.1701	.	.	ID=Chr1:SNP:62841;Variant_seq=G;Reference_seq=T;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62852	62852	17.1701	.	.	ID=Chr1:SNP:62852;Variant_seq=G;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	62929	62929	17.1701	.	.	ID=Chr1:SNP:62929;Variant_seq=A;Reference_seq=C;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	63049	63049	17.1701	.	.	ID=Chr1:SNP:63049;Variant_seq=T;Reference_seq=A;Total_reads=1;Zygosity=1:HOM_mut 
+Chr1	SAMTOOLS	SNP	63120	63120	4.77465	.	.	ID=Chr1:SNP:63120;Variant_seq=A;Reference_seq=C;Total_reads=2;Zygosity=2:HET