Mercurial > repos > john-mccallum > pcr_markers
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