Mercurial > repos > john-mccallum > pcr_markers

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

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author ben-warren
date Thu, 22 May 2014 20:30:19 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/targets.gff	Thu May 22 20:30:19 2014 -0400
@@ -0,0 +1,31 @@
+k69_93535	SAMTOOLS	INDEL	3	7	4.44	.	.	ID=k69_93535:SAMTOOLS:INDEL:3;Variant_seq=ATTTCACATCCCATCATCA,ATCACATCCCATCATCA;Reference_seq=ATCA;INDEL;DP=5;VDB=0.0149;AF1=1;AC1=24;DP4=0,0,3,0;MQ=23;FQ=-33.2
+k69_93535	SAMTOOLS	INDEL	5	6	4.91	.	.	ID=k69_93535:SAMTOOLS:INDEL:5;Variant_seq=CTCATATCCCATCATC,CCGGCC;Reference_seq=C;INDEL;DP=6;VDB=0.0137;AF1=1;AC1=24;DP4=0,0,3,1;MQ=17;FQ=-32.4
+k69_93535	SAMTOOLS	SNP	1141	1142	999	.	.	ID=k69_93535:SAMTOOLS:SNP:1141;Variant_seq=T;Reference_seq=C;DP=2644;VDB=0.0374;AF1=0.1882;AC1=5;DP4=748,786,225,294;MQ=42;FQ=999;PV4=0.037,0,0.036,0.39
+k69_93535	SAMTOOLS	SNP	1147	1148	999	.	.	ID=k69_93535:SAMTOOLS:SNP:1147;Variant_seq=G;Reference_seq=C;DP=2645;VDB=0.0371;AF1=0.3527;G3=0.2771,0.7229,6.934e-153;HWE=0.0248;AC1=8;DP4=733,804,447,519;MQ=42;FQ=999;PV4=0.51,0,0.027,1
+k69_93535	SAMTOOLS	SNP	1336	1337	999	.	.	ID=k69_93535:SAMTOOLS:SNP:1336;Variant_seq=A;Reference_seq=G;DP=2211;VDB=0.0395;AF1=0.4583;G3=0.08329,0.9167,1.041e-76;HWE=0.000925;AC1=11;DP4=487,645,470,542;MQ=35;FQ=999;PV4=0.12,0,0.00016,0.36
+k69_93535	SAMTOOLS	SNP	3	4	27.6	.	.	ID=k69_93535:SAMTOOLS:SNP:3;Variant_seq=T;Reference_seq=A;DP=5;VDB=0.0198;AF1=1;AC1=24;DP4=1,0,3,1;MQ=19;FQ=-24.6;PV4=1,1,1,1
+k69_93535	SAMTOOLS	SNP	661	662	999	.	.	ID=k69_93535:SAMTOOLS:SNP:661;Variant_seq=G;Reference_seq=A;DP=1941;VDB=0.0388;AF1=0.4584;G3=0.08304,0.917,5.651e-77;HWE=0.000923;AC1=11;DP4=553,528,368,347;MQ=42;FQ=999;PV4=0.92,0,1,1
+k69_93535	SAMTOOLS	SNP	751	752	999	.	.	ID=k69_93535:SAMTOOLS:SNP:751;Variant_seq=A;Reference_seq=G;DP=1870;VDB=0.0363;AF1=0.5;G3=3.472e-15,1,5e-52;HWE=4.53e-05;AC1=12;DP4=512,544,345,364;MQ=42;FQ=999;PV4=0.96,6.1e-38,0.014,1
+k69_93535	SAMTOOLS	SNP	887	888	999	.	.	ID=k69_93535:SAMTOOLS:SNP:887;Variant_seq=G;Reference_seq=A;DP=2583;VDB=0.0394;AF1=0.4583;G3=0.08333,0.9167,8.95e-52;HWE=0.000926;AC1=11;DP4=790,493,590,361;MQ=42;FQ=999;PV4=0.83,0.069,0.41,1
+k69_98089	SAMTOOLS	INDEL	2	6	999	.	.	ID=k69_98089:SAMTOOLS:INDEL:2;Variant_seq=CAACAAA,CAAACAAA,CAAAAACAAA;Reference_seq=CAAA;INDEL;DP=430;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,182,1;MQ=39;FQ=-71.8
+k69_98089	SAMTOOLS	INDEL	3	6	999	.	.	ID=k69_98089:SAMTOOLS:INDEL:3;Variant_seq=AAAAAACAAA,AAAA;Reference_seq=AAA;INDEL;DP=451;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,214,1;MQ=39;FQ=-48
+k69_98089	SAMTOOLS	INDEL	4	6	999	.	.	ID=k69_98089:SAMTOOLS:INDEL:4;Variant_seq=AAACACTAAAAACAAA,AAA;Reference_seq=AA;INDEL;DP=468;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,219,1;MQ=39;FQ=-49.3
+k69_98089	SAMTOOLS	INDEL	5	6	999	.	.	ID=k69_98089:SAMTOOLS:INDEL:5;Variant_seq=AACTAAAAACAAA;Reference_seq=A;INDEL;DP=534;VDB=0.0000;AF1=1;AC1=24;DP4=0,0,220,1;MQ=39;FQ=-77.6
+k69_98089	SAMTOOLS	INDEL	722	723	131	.	.	ID=k69_98089:SAMTOOLS:INDEL:722;Variant_seq=TAAAAAA;Reference_seq=T;INDEL;DP=220;VDB=0.0006;AF1=0.3195;G3=0.299,0.701,1.118e-32;HWE=0.0406;AC1=8;DP4=4,52,0,27;MQ=38;FQ=133;PV4=0.3,1,5.4e-16,0.00096
+k69_98089	SAMTOOLS	INDEL	726	727	69.7	.	.	ID=k69_98089:SAMTOOLS:INDEL:726;Variant_seq=TAAAAA;Reference_seq=T;INDEL;DP=152;VDB=0.0007;AF1=0.2294;AC1=5;DP4=4,30,1,6;MQ=40;FQ=70.8;PV4=1,0.025,0.0063,0.079
+k69_98089	SAMTOOLS	INDEL	729	731	71.6	.	.	ID=k69_98089:SAMTOOLS:INDEL:729;Variant_seq=TAAAAAAA;Reference_seq=TA;INDEL;DP=104;VDB=0.0010;AF1=0.3359;AC1=8;DP4=3,15,0,4;MQ=40;FQ=73.4;PV4=1,1,1,1
+k69_98089	SAMTOOLS	INDEL	741	748	48.2	.	.	ID=k69_98089:SAMTOOLS:INDEL:741;Variant_seq=AATTTCTATTTGTTTATTATTTCT,AATTTCTATTTGTTTATTTCT,AATTTCTATTTCT;Reference_seq=AATTTCT;INDEL;DP=18;VDB=0.0050;AF1=1;AC1=24;DP4=0,0,0,9;MQ=27;FQ=-35
+k69_98089	SAMTOOLS	INDEL	742	748	5.8	.	.	ID=k69_98089:SAMTOOLS:INDEL:742;Variant_seq=ATTTTTCT,ATTTCTATTTTCT,ATTTCTATTTTTCT;Reference_seq=ATTTCT;INDEL;DP=17;VDB=0.0022;AF1=1;AC1=24;DP4=0,0,0,3;MQ=36;FQ=-31.8
+k69_98089	SAMTOOLS	INDEL	743	748	86.5	.	.	ID=k69_98089:SAMTOOLS:INDEL:743;Variant_seq=TTTCTATTTGTTCT,TTTCTATTTGTTTATTATTCT,TTTCTATTTGTTTATTCT;Reference_seq=TTTCT;INDEL;DP=16;VDB=0.0021;AF1=1;AC1=24;DP4=0,0,0,8;MQ=29;FQ=-34.7
+k69_98089	SAMTOOLS	SNP	2	3	999	.	.	ID=k69_98089:SAMTOOLS:SNP:2;Variant_seq=A;Reference_seq=C;DP=430;VDB=0.0000;AF1=0.5;G3=1.09e-24,1,5.6e-21;HWE=4.53e-05;AC1=12;DP4=207,1,212,1;MQ=40;FQ=999;PV4=1,1,0.00045,1
+k69_98089	SAMTOOLS	SNP	30	31	999	.	.	ID=k69_98089:SAMTOOLS:SNP:30;Variant_seq=G;Reference_seq=T;DP=1858;VDB=0.0011;AF1=0.5417;G3=2.023e-19,0.9167,0.08333;HWE=0.000926;AC1=13;DP4=624,74,985,116;MQ=41;FQ=999;PV4=1,0,0.00089,1
+k69_98089	SAMTOOLS	SNP	3	4	999	.	.	ID=k69_98089:SAMTOOLS:SNP:3;Variant_seq=C;Reference_seq=A;DP=451;VDB=0.0000;AF1=0.5;G3=3.935e-24,1,2.231e-22;HWE=4.53e-05;AC1=12;DP4=226,8,205,1;MQ=40;FQ=999;PV4=0.041,1,0.00055,1
+k69_98089	SAMTOOLS	SNP	453	454	31.2	.	.	ID=k69_98089:SAMTOOLS:SNP:453;Variant_seq=T;Reference_seq=A;DP=3692;VDB=0.0394;AF1=0.04171;AC1=1;DP4=649,868,130,171;MQ=39;FQ=31.4;PV4=0.9,0,2.3e-293,0.00051
+k69_98089	SAMTOOLS	SNP	515	516	999	.	.	ID=k69_98089:SAMTOOLS:SNP:515;Variant_seq=G;Reference_seq=A;DP=4455;VDB=0.0378;AF1=0.4583;G3=0.08333,0.9167,1.498e-16;HWE=0.000926;AC1=11;DP4=952,817,1390,1120;MQ=33;FQ=999;PV4=0.32,0,0,1
+k69_98089	SAMTOOLS	SNP	522	523	999	.	.	ID=k69_98089:SAMTOOLS:SNP:522;Variant_seq=G;Reference_seq=A;DP=4698;VDB=0.0388;AF1=0.4168;G3=0.1656,0.8344,2.693e-36;HWE=0.00483;AC1=10;DP4=958,914,1327,1222;MQ=35;FQ=999;PV4=0.56,0,0,1
+k69_98089	SAMTOOLS	SNP	550	551	999	.	.	ID=k69_98089:SAMTOOLS:SNP:550;Variant_seq=A;Reference_seq=G;DP=4866;VDB=0.0385;AF1=0.5417;G3=2.024e-12,0.9167,0.08333;HWE=0.000926;AC1=13;DP4=1034,806,1547,1233;MQ=38;FQ=999;PV4=0.72,0,1e-231,1
+k69_98089	SAMTOOLS	SNP	625	626	999	.	.	ID=k69_98089:SAMTOOLS:SNP:625;Variant_seq=G;Reference_seq=A;DP=3557;VDB=0.0340;AF1=0.5;G3=8.721e-11,1,5.503e-15;HWE=4.53e-05;AC1=12;DP4=478,825,742,1369;MQ=41;FQ=999;PV4=0.38,0,2.7e-35,0.0059
+k69_98089	SAMTOOLS	SNP	693	694	999	.	.	ID=k69_98089:SAMTOOLS:SNP:693;Variant_seq=A;Reference_seq=T;DP=743;VDB=0.0038;AF1=0.5;G3=1.826e-14,1,3.643e-17;HWE=4.53e-05;AC1=12;DP4=37,238,66,367;MQ=39;FQ=999;PV4=0.58,6.3e-295,5.1e-12,1
+k69_98089	SAMTOOLS	SNP	717	718	999	.	.	ID=k69_98089:SAMTOOLS:SNP:717;Variant_seq=C;Reference_seq=T;DP=284;VDB=0.0010;AF1=0.5001;G3=2.555e-19,1,4.593e-12;HWE=4.54e-05;AC1=12;DP4=5,91,8,138;MQ=36;FQ=999;PV4=1,1.9e-90,2.7e-07,6.5e-05
+k69_98089	SAMTOOLS	SNP	723	724	999	.	.	ID=k69_98089:SAMTOOLS:SNP:723;Variant_seq=A;Reference_seq=G;DP=193;VDB=0.0010;AF1=0.4433;G3=0.08685,0.9132,1.287e-11;HWE=0.0015;AC1=11;DP4=5,79,5,45;MQ=37;FQ=999;PV4=0.5,2.9e-13,0.00011,0.47
+k69_98089	SAMTOOLS	SNP	726	727	999	.	.	ID=k69_98089:SAMTOOLS:SNP:726;Variant_seq=C;Reference_seq=T;DP=152;VDB=0.0008;AF1=0.4943;G3=0.0835,0.8466,0.06993;HWE=0.0149;AC1=12;DP4=4,49,5,32;MQ=36;FQ=999;PV4=0.48,5.3e-32,0.00016,0.43