source: trunk/test/data/small.gff3 @ 2450

Last change on this file since 2450 was 2450, checked in by Peter, 12 years ago

test gff3 file. refs #647
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1##gff-version 3
2##List of SNPs. Date Mon Nov  1 15:06:39 2010    Stringency: medium Mate Pair: 0 Read Length: 50 Polymorphism Rate: 0.001000 Bayes Coverage: 60 Bayes_Single_SNP: 1 Filter_Single_SNP: 1 Quick_P_Threshold: 0.997000 Bayes_P_Threshold: 0.040000 Minimum_Allele_Ratio: 0.150000 Minimum_Allele_Ratio_Multiple_of_Dicolor_Error: 100
3##chr1  chr1
4##chr2  chr2
5##chr3  chr3
6##chr4  chr4
7##chr5  chr5
8##chr6  chr6
9##chr7  chr7
10##chr8  chr8
11##chr9  chr9
12##chr10 chr10
13##chr11 chr11
14##chr12 chr12
15##chr13 chr13
16##chr14 chr14
17##chr15 chr15
18##chr16 chr16
19##chr17 chr17
20##chr18 chr18
21##chr19 chr19
22##chr20 chr20
23##chr21 chr21
24##chr22 chr22
25##chr23 chrX
26##chr24 chrY
27##chr25 chrM
28##Data source:    Experiment: small_F3
29##Data source:    Experiment: small_F3
30##Data source:    Experiment: small_F3
31##Data source:    Experiment: small_F3
32##Data source:    Experiment: small_F3
33##Data source:    Experiment: small_F3
34##Data source:    Experiment: small_F3
35##Data source:    Experiment: small_F3
36##Data source:    Experiment: small_F3
37##Data source:    Experiment: small_F3
38##Data source:    Experiment: small_F3
39##Data source:    Experiment: small_F3
40##Data source:    Experiment: small_F3
41##Data source:    Experiment: small_F3
42##Data source:    Experiment: small_F3
43##Data source:    Experiment: small_F3
44##Data source:    Experiment: small_F3
45##Data source:    Experiment: small_F3
46##Data source:    Experiment: small_F3
47##Data source:    Experiment: small_F3
48##Data source:    Experiment: small_F3
49##Data source:    Experiment: small_F3
50##Data source:    Experiment: small_F3
51##Data source:    Experiment: small_F3
52##Data source:    Experiment: small_F3
53#Chr  Source  Type  Pos_Start Pos_End Score Strand  Phase Attributes
54chr3  SOLiD_diBayes SNP 904531  904531  0.000015  . . genotype=T;reference=C;coverage=5;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=4;novelAlleleStarts=4;novelAlleleMeanQV=19;diColor1=30;diColor2=30;het=0;flag=h4,h10,h9,
55chr3  SOLiD_diBayes SNP 969190  969190  0.062500  . . genotype=T;reference=C;coverage=2;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=29;diColor1=31;diColor2=31;het=0;flag=h4,h10,
56chr3  SOLiD_diBayes SNP 976355  976355  0.062500  . . genotype=T;reference=C;coverage=2;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=21;diColor1=23;diColor2=23;het=0;flag=h4,h10,
57chr3  SOLiD_diBayes SNP 977664  977664  0.000000  . . genotype=G;reference=A;coverage=7;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=7;novelAlleleStarts=6;novelAlleleMeanQV=22;diColor1=00;diColor2=00;het=0;flag=h4,h10,
58chr3  SOLiD_diBayes SNP 979502  979502  0.000000  . . genotype=C;reference=T;coverage=10;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=10;novelAlleleStarts=9;novelAlleleMeanQV=23;diColor1=02;diColor2=02;het=0;flag=h4,h10,
59chr3  SOLiD_diBayes SNP 979522  979522  0.000000  . . genotype=C;reference=T;coverage=11;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=11;novelAlleleStarts=6;novelAlleleMeanQV=26;diColor1=10;diColor2=10;het=0;flag=h4,h10,
60chr3  SOLiD_diBayes SNP 992323  992323  0.000934  . . genotype=S;reference=G;coverage=11;refAlleleCounts=4;refAlleleStarts=3;refAlleleMeanQV=19;novelAlleleCounts=7;novelAlleleStarts=7;novelAlleleMeanQV=19;diColor1=01;diColor2=32;het=1;flag=
61chr3  SOLiD_diBayes SNP 992334  992334  0.000656  . . genotype=R;reference=G;coverage=13;refAlleleCounts=9;refAlleleStarts=9;refAlleleMeanQV=21;novelAlleleCounts=4;novelAlleleStarts=3;novelAlleleMeanQV=26;diColor1=11;diColor2=33;het=1;flag=
62chr3  SOLiD_diBayes SNP 997200  997200  0.001043  . . genotype=Y;reference=C;coverage=10;refAlleleCounts=5;refAlleleStarts=5;refAlleleMeanQV=21;novelAlleleCounts=4;novelAlleleStarts=2;novelAlleleMeanQV=27;diColor1=11;diColor2=33;het=1;flag=
63chr3  SOLiD_diBayes SNP 990260  990260  0.062500  . . genotype=T;reference=C;coverage=2;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=19;diColor1=31;diColor2=31;het=0;flag=h4,h10,
64chr3  SOLiD_diBayes SNP 999631  999631  0.000000  . . genotype=G;reference=A;coverage=12;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=11;novelAlleleStarts=9;novelAlleleMeanQV=26;diColor1=00;diColor2=00;het=0;flag=h4,h10,h9,
65chr3  SOLiD_diBayes SNP 933331  933331  0.000000  . . genotype=Y;reference=T;coverage=23;refAlleleCounts=13;refAlleleStarts=12;refAlleleMeanQV=28;novelAlleleCounts=9;novelAlleleStarts=7;novelAlleleMeanQV=19;diColor1=01;diColor2=23;het=1;flag=
66chr3  SOLiD_diBayes SNP 933550  933550  0.043630  . . genotype=S;reference=G;coverage=5;refAlleleCounts=2;refAlleleStarts=2;refAlleleMeanQV=27;novelAlleleCounts=3;novelAlleleStarts=2;novelAlleleMeanQV=17;diColor1=02;diColor2=31;het=1;flag=
67chr3  SOLiD_diBayes SNP 939733  939733  0.444487  . . genotype=G;reference=C;coverage=3;refAlleleCounts=1;refAlleleStarts=1;refAlleleMeanQV=5;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=21;diColor1=30;diColor2=30;het=0;flag= 
68chr3  SOLiD_diBayes SNP 939916  939916  0.000358  . . genotype=S;reference=C;coverage=14;refAlleleCounts=5;refAlleleStarts=5;refAlleleMeanQV=15;novelAlleleCounts=9;novelAlleleStarts=8;novelAlleleMeanQV=21;diColor1=00;diColor2=33;het=1;flag=
69chr3  SOLiD_diBayes SNP 939099  939099  0.062500  . . genotype=A;reference=G;coverage=2;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=25;diColor1=21;diColor2=21;het=0;flag=h4,h10,
70chr3  SOLiD_diBayes SNP 939471  939471  0.079193  . . genotype=R;reference=G;coverage=8;refAlleleCounts=6;refAlleleStarts=5;refAlleleMeanQV=24;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=27;diColor1=01;diColor2=23;het=1;flag=
71chr3  SOLiD_diBayes SNP 939799  939799  0.000000  . . genotype=Y;reference=C;coverage=17;refAlleleCounts=8;refAlleleStarts=7;refAlleleMeanQV=20;novelAlleleCounts=9;novelAlleleStarts=7;novelAlleleMeanQV=21;diColor1=03;diColor2=21;het=1;flag=
72chr3  SOLiD_diBayes SNP 967193  967193  0.062500  . . genotype=C;reference=T;coverage=2;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=15;diColor1=30;diColor2=30;het=0;flag=h4,h10,
73chr3  SOLiD_diBayes SNP 974710  974710  0.001982  . . genotype=S;reference=G;coverage=7;refAlleleCounts=3;refAlleleStarts=2;refAlleleMeanQV=29;novelAlleleCounts=4;novelAlleleStarts=4;novelAlleleMeanQV=18;diColor1=00;diColor2=33;het=1;flag=
74chr3  SOLiD_diBayes SNP 974751  974751  0.093300  . . genotype=R;reference=A;coverage=10;refAlleleCounts=8;refAlleleStarts=3;refAlleleMeanQV=27;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=27;diColor1=13;diColor2=31;het=1;flag=
75chr3  SOLiD_diBayes SNP 977063  977063  0.000000  . . genotype=Y;reference=C;coverage=23;refAlleleCounts=9;refAlleleStarts=7;refAlleleMeanQV=17;novelAlleleCounts=14;novelAlleleStarts=12;novelAlleleMeanQV=27;diColor1=13;diColor2=31;het=1;flag=
76chr3  SOLiD_diBayes SNP 1108138 1108138 0.062500  . . genotype=T;reference=C;coverage=2;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=29;diColor1=13;diColor2=13;het=0;flag=h4,h10,
77chr3  SOLiD_diBayes SNP 1110233 1110233 0.000000  . . genotype=S;reference=C;coverage=31;refAlleleCounts=24;refAlleleStarts=18;refAlleleMeanQV=23;novelAlleleCounts=7;novelAlleleStarts=6;novelAlleleMeanQV=21;diColor1=11;diColor2=22;het=1;flag=
78chr3  SOLiD_diBayes SNP 1149494 1149494 0.000000  . . genotype=G;reference=A;coverage=78;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=77;novelAlleleStarts=33;novelAlleleMeanQV=26;diColor1=31;diColor2=31;het=0;flag=h4,h10,h9,
79chr3  SOLiD_diBayes SNP 1153994 1153994 0.000340  . . genotype=R;reference=A;coverage=26;refAlleleCounts=6;refAlleleStarts=4;refAlleleMeanQV=22;novelAlleleCounts=18;novelAlleleStarts=13;novelAlleleMeanQV=24;diColor1=13;diColor2=31;het=1;flag=
80chr3  SOLiD_diBayes SNP 1153935 1153935 0.000152  . . genotype=Y;reference=C;coverage=16;refAlleleCounts=6;refAlleleStarts=6;refAlleleMeanQV=13;novelAlleleCounts=10;novelAlleleStarts=9;novelAlleleMeanQV=18;diColor1=13;diColor2=31;het=1;flag=
81chr3  SOLiD_diBayes SNP 1245896 1245896 0.177945  . . genotype=T;reference=C;coverage=4;refAlleleCounts=1;refAlleleStarts=1;refAlleleMeanQV=4;novelAlleleCounts=3;novelAlleleStarts=3;novelAlleleMeanQV=13;diColor1=22;diColor2=22;het=0;flag= 
82chr3  SOLiD_diBayes SNP 1259949 1259949 0.062500  . . genotype=T;reference=C;coverage=3;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=7;diColor1=21;diColor2=21;het=0;flag=h4,h10,h9,h15,
83chr3  SOLiD_diBayes SNP 1263517 1263517 0.421128  . . genotype=G;reference=C;coverage=6;refAlleleCounts=1;refAlleleStarts=1;refAlleleMeanQV=18;novelAlleleCounts=5;novelAlleleStarts=5;novelAlleleMeanQV=17;diColor1=02;diColor2=02;het=0;flag= 
84chr3  SOLiD_diBayes SNP 1265919 1265919 0.078474  . . genotype=Y;reference=C;coverage=6;refAlleleCounts=2;refAlleleStarts=2;refAlleleMeanQV=27;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=8;diColor1=12;diColor2=30;het=1;flag=
85chr3  SOLiD_diBayes SNP 1269100 1269100 0.003906  . . genotype=C;reference=T;coverage=3;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=3;novelAlleleStarts=2;novelAlleleMeanQV=16;diColor1=13;diColor2=13;het=0;flag=h4,h10,
86chr3  SOLiD_diBayes SNP 1312517 1312517 0.043482  . . genotype=Y;reference=C;coverage=10;refAlleleCounts=3;refAlleleStarts=3;refAlleleMeanQV=10;novelAlleleCounts=6;novelAlleleStarts=6;novelAlleleMeanQV=18;diColor1=11;diColor2=33;het=1;flag=
87chr3  SOLiD_diBayes SNP 1320599 1320599 0.062500  . . genotype=G;reference=A;coverage=2;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=17;diColor1=30;diColor2=30;het=0;flag=h4,h10,
88chr3  SOLiD_diBayes SNP 1320922 1320922 0.000000  . . genotype=Y;reference=C;coverage=24;refAlleleCounts=14;refAlleleStarts=12;refAlleleMeanQV=22;novelAlleleCounts=7;novelAlleleStarts=6;novelAlleleMeanQV=18;diColor1=01;diColor2=23;het=1;flag=
89chr3  SOLiD_diBayes SNP 1320929 1320929 0.024253  . . genotype=R;reference=G;coverage=5;refAlleleCounts=3;refAlleleStarts=3;refAlleleMeanQV=10;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=29;diColor1=13;diColor2=31;het=1;flag=
90chr3  SOLiD_diBayes SNP 1327402 1327402 0.000000  . . genotype=W;reference=T;coverage=137;refAlleleCounts=80;refAlleleStarts=37;refAlleleMeanQV=16;novelAlleleCounts=44;novelAlleleStarts=23;novelAlleleMeanQV=19;diColor1=11;diColor2=22;het=1;flag=
91chr3  SOLiD_diBayes SNP 1377530 1377530 0.000000  . . genotype=G;reference=C;coverage=9;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=9;novelAlleleStarts=6;novelAlleleMeanQV=21;diColor1=03;diColor2=03;het=0;flag=h4,h10,
92chr3  SOLiD_diBayes SNP 1377599 1377599 0.003020  . . genotype=R;reference=A;coverage=18;refAlleleCounts=11;refAlleleStarts=10;refAlleleMeanQV=18;novelAlleleCounts=4;novelAlleleStarts=4;novelAlleleMeanQV=22;diColor1=11;diColor2=33;het=1;flag=
93chr3  SOLiD_diBayes SNP 1377627 1377627 0.009379  . . genotype=R;reference=G;coverage=8;refAlleleCounts=4;refAlleleStarts=4;refAlleleMeanQV=17;novelAlleleCounts=3;novelAlleleStarts=3;novelAlleleMeanQV=22;diColor1=10;diColor2=32;het=1;flag=
94chr3  SOLiD_diBayes SNP 1377754 1377754 0.062500  . . genotype=G;reference=A;coverage=2;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=31;diColor1=11;diColor2=11;het=0;flag=h4,h10,
95chr3  SOLiD_diBayes SNP 1382276 1382276 0.006750  . . genotype=M;reference=A;coverage=6;refAlleleCounts=3;refAlleleStarts=3;refAlleleMeanQV=23;novelAlleleCounts=3;novelAlleleStarts=2;novelAlleleMeanQV=25;diColor1=23;diColor2=32;het=1;flag=
96chr3  SOLiD_diBayes SNP 1382314 1382314 0.017644  . . genotype=Y;reference=C;coverage=15;refAlleleCounts=9;refAlleleStarts=7;refAlleleMeanQV=21;novelAlleleCounts=3;novelAlleleStarts=2;novelAlleleMeanQV=22;diColor1=03;diColor2=21;het=1;flag=
97chr3  SOLiD_diBayes SNP 1411394 1411394 0.339961  . . genotype=A;reference=C;coverage=3;refAlleleCounts=1;refAlleleStarts=1;refAlleleMeanQV=4;novelAlleleCounts=2;novelAlleleStarts=2;novelAlleleMeanQV=24;diColor1=10;diColor2=10;het=0;flag= 
98chr3  SOLiD_diBayes SNP 1411597 1411597 0.000015  . . genotype=C;reference=G;coverage=4;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=4;novelAlleleStarts=4;novelAlleleMeanQV=24;diColor1=02;diColor2=02;het=0;flag=h4,h10,
99chr3  SOLiD_diBayes SNP 1411779 1411779 0.000024  . . genotype=Y;reference=T;coverage=17;refAlleleCounts=11;refAlleleStarts=6;refAlleleMeanQV=23;novelAlleleCounts=6;novelAlleleStarts=4;novelAlleleMeanQV=27;diColor1=02;diColor2=20;het=1;flag=
100chr3  SOLiD_diBayes SNP 1413130 1413130 0.000015  . . genotype=G;reference=A;coverage=5;refAlleleCounts=0;refAlleleStarts=0;refAlleleMeanQV=0;novelAlleleCounts=4;novelAlleleStarts=3;novelAlleleMeanQV=19;diColor1=30;diColor2=30;het=0;flag=h4,h10,h9,
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