Mercurial > repos > greg > call_amr_mutations

comparison test-data/input1.vcf @ 1:52a9e19ae588 draft

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author greg
date Mon, 20 Feb 2023 19:56:50 +0000
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0:64999b5b58fe 1:52a9e19ae588
1 Chrom Position Ref Cons Reads1 Reads2 VarFreq Strands1 Strands2 Qual1 Qual2 Pvalue MapQual1 MapQual2 Reads1Plus Reads1Minus Reads2Plus Reads2Minus VarAllele
2 chromosome 6848 C T 0 46 100% 0 2 0 18 2.434301551680221E-27 0 1 0 0 14 32 T
3 chromosome 28975 G A 0 19 100% 0 2 0 16 2.829233375250701E-11 0 1 0 0 16 3 A
4 chromosome 64632 T C 1 20 95.24% 1 2 17 17 4.087260223157705E-11 1 1 1 0 9 11 C
5 chromosome 73738 T C 0 15 100% 0 2 0 16 6.446725037893782E-9 0 1 0 0 12 3 C
6 chromosome 122896 G A 0 29 100% 0 2 0 21 3.325875998788469E-17 0 1 0 0 3 26 A
7 chromosome 171823 C T 1 20 90.91% 1 2 15 19 4.087260223157705E-11 1 1 1 0 17 3 T
8 chromosome 182106 C T 0 15 100% 0 2 0 16 6.446725037893782E-9 0 1 0 0 6 9 T
9 chromosome 200731 C T 2 47 95.92% 1 2 22 20 5.0043936105136293E-26 1 1 2 0 21 26 T
10 chromosome 240050 T C 0 30 93.75% 0 2 0 19 8.455616946072207E-18 0 1 0 0 14 16 C
11 chromosome 243867 C T 0 33 100% 0 2 0 19 1.3851512057218843E-19 0 1 0 0 24 9 T
12 chromosome 245190 C T 0 42 93.33% 0 2 0 18 5.9562436962098315E-25 0 1 0 0 24 18 T
13 chromosome 274236 C A 0 59 100% 0 2 0 20 4.105646544903784E-35 0 1 0 0 21 38 A
14 chromosome 317131 G T 1 7 87.5% 1 1 21 18 6.993006993006951E-4 1 1 1 0 7 0 T
15 chromosome 318187 C T 0 39 100% 0 2 0 21 3.6741722220670473E-23 0 1 0 0 17 22 T
16 chromosome 337241 T C 0 39 95.12% 0 2 0 20 3.6741722220670473E-23 0 1 0 0 19 20 C
17 chromosome 359536 G A 0 18 100% 0 2 0 16 1.1019119461502356E-10 0 1 0 0 5 13 A
18 chromosome 387637 G A 0 27 100% 0 2 0 19 5.136266628670978E-16 0 1 0 0 15 12 A
19 chromosome 433277 G T 0 19 100% 0 2 0 19 2.829233375250701E-11 0 1 0 0 10 9 T
20 chromosome 513052 C T 0 16 100% 0 2 0 18 1.6636709775210046E-9 0 1 0 0 2 14 T
21 chromosome 521963 A G 1 57 91.94% 1 2 19 21 9.60721291507612E-33 1 1 1 0 26 31 G
22 chromosome 571199 G A 3 17 85% 1 2 16 21 1.2847621301458368E-8 1 1 0 3 7 10 A
23 chromosome 644625 T C 1 21 95.45% 1 2 22 18 1.093104478286346E-11 1 1 0 1 10 11 C
24 chromosome 665308 T C 1 16 94.12% 1 2 17 17 7.713383623051864E-9 1 1 1 0 7 9 C
25 chromosome 692932 C T 1 20 95.24% 1 2 19 17 4.087260223157705E-11 1 1 0 1 5 15 T
26 chromosome 702761 G C 0 20 95.24% 0 2 0 18 7.254444551924877E-12 0 1 0 0 13 7 C
27 chromosome 706839 C T 0 7 100% 0 2 0 20 2.9137529137529E-4 0 1 0 0 4 3 T
28 chromosome 732173 A T 0 20 100% 0 2 0 18 7.254444551924877E-12 0 1 0 0 10 10 T
29 chromosome 765499 A C 0 27 100% 0 2 0 18 5.136266628670978E-16 0 1 0 0 24 3 C
30 chromosome 789298 G A 0 18 100% 0 2 0 16 1.1019119461502356E-10 0 1 0 0 9 9 A
31 chromosome 814684 T G 4 22 81.48% 1 2 18 17 5.52610926578708E-11 1 1 4 0 11 11 G
32 chromosome 852207 T G 0 13 100% 0 2 0 17 9.614829913658729E-8 0 1 0 0 8 5 G
33 chromosome 867050 A C 0 14 93.33% 0 2 0 18 2.4927336813189342E-8 0 1 0 0 9 5 C
34 chromosome 1023150 A G 0 27 100% 0 2 0 17 5.136266628670978E-16 0 1 0 0 11 16 G
35 chromosome 1120096 C T 0 55 100% 0 2 0 20 1.0149479655659631E-32 0 1 0 0 19 36 T
36 chromosome 1131906 T C 0 27 100% 0 2 0 17 5.136266628670978E-16 0 1 0 0 11 16 C
37 chromosome 1181950 A G 1 36 97.3% 1 2 16 18 2.176240469993604E-20 1 1 0 1 21 15 G
38 chromosome 1184347 G A 1 18 90% 1 2 15 21 5.658466750501197E-10 1 1 0 1 5 13 A
39 chromosome 1223198 C T 0 27 100% 0 2 0 20 5.136266628670978E-16 0 1 0 0 6 21 T
40 chromosome 1270555 G T 0 15 93.75% 0 2 0 18 6.446725037893782E-9 0 1 0 0 4 11 T
41 chromosome 1306861 C T 0 31 100% 0 2 0 19 2.148558404330002E-18 0 1 0 0 17 14 T
42 chromosome 1377487 G A 1 12 92.31% 1 2 18 20 1.3460761879122365E-6 1 1 0 1 8 4 A
43 chromosome 1385721 G A 0 38 100% 0 2 0 19 1.4508269799957698E-22 0 1 0 0 18 20 A
44 chromosome 1406212 C T 0 28 100% 0 2 0 19 1.3074133236616653E-16 0 1 0 0 15 13 T
45 chromosome 1423420 A G 0 16 94.12% 0 2 0 18 1.6636709775210046E-9 0 1 0 0 1 15 G
46 chromosome 1481095 C T 0 9 100% 0 1 0 22 2.056766762649123E-5 0 1 0 0 9 0 T
47 chromosome 1481116 C T 0 12 100% 0 1 0 18 3.6980115052534125E-7 0 1 0 0 12 0 T
48 chromosome 1592398 C A 0 26 100% 0 2 0 20 2.016460231996677E-15 0 1 0 0 1 25 A
49 chromosome 1621512 C A 0 27 100% 0 2 0 19 5.136266628670978E-16 0 1 0 0 4 23 A
50 chromosome 1631941 G T 0 24 100% 0 2 0 18 3.101005612159882E-14 0 1 0 0 14 10 T
51 chromosome 1728049 G A 1 17 94.44% 1 2 15 17 2.0936326976854063E-9 1 1 1 0 8 9 A
52 chromosome 1774177 C T 0 27 100% 0 2 0 17 5.136266628670978E-16 0 1 0 0 16 11 T
53 chromosome 1781207 C T 0 6 85.71% 0 2 0 22 0.0010822510822510842 0 1 0 0 3 3 T
54 chromosome 1797708 T C 0 21 100% 0 2 0 19 1.8578455559807287E-12 0 1 0 0 8 13 C
55 chromosome 1798769 G T 1 22 95.65% 1 2 22 18 2.914945275430307E-12 1 1 0 1 9 13 T
56 chromosome 1867996 T C 0 15 100% 0 2 0 17 6.446725037893782E-9 0 1 0 0 7 8 C
57 chromosome 1982986 C T 0 26 100% 0 2 0 20 2.016460231996677E-15 0 1 0 0 15 11 T
58 chromosome 2067935 G A 0 17 100% 0 2 0 19 4.2852131239177147E-10 0 1 0 0 6 11 A
59 chromosome 2133680 G T 0 24 100% 0 2 0 18 3.101005612159882E-14 0 1 0 0 13 11 T
60 chromosome 2179870 T C 2 12 85.71% 1 2 18 19 2.9912804175827393E-6 1 1 2 0 5 7 C
61 chromosome 2280814 A C 1 7 87.5% 1 2 15 18 6.993006993006951E-4 1 1 1 0 6 1 C
62 chromosome 2299647 A G 0 8 100% 0 2 0 20 7.770007770007759E-5 0 1 0 0 4 4 G
63 chromosome 2371243 T C 0 17 100% 0 2 0 17 4.2852131239177147E-10 0 1 0 0 9 8 C
64 chromosome 2423657 A G 1 19 90.48% 1 2 16 18 1.5234333559041912E-10 1 1 1 0 6 13 G
65 chromosome 2694862 G A 2 15 88.24% 1 1 16 19 7.327714441899113E-8 1 1 0 2 15 0 A
66 chromosome 2749671 A G 0 27 96.43% 0 2 0 20 5.136266628670978E-16 0 1 0 0 8 19 G
67 chromosome 2834318 G A 0 20 100% 0 2 0 18 7.254444551924877E-12 0 1 0 0 4 16 A
68 chromosome 2956135 G A 0 15 100% 0 2 0 18 6.446725037893782E-9 0 1 0 0 8 7 A
69 chromosome 2989856 G A 0 28 100% 0 2 0 23 1.3074133236616653E-16 0 1 0 0 12 16 A
70 chromosome 3038888 T C 2 21 87.5% 2 2 15 18 3.643681594287794E-11 1 1 1 1 9 12 C
71 chromosome 3163858 A G 0 21 100% 0 2 0 17 1.8578455559807287E-12 0 1 0 0 8 13 G
72 chromosome 3306423 C T 0 19 100% 0 2 0 18 2.829233375250701E-11 0 1 0 0 12 7 T
73 chromosome 3364887 G A 0 15 100% 0 2 0 20 6.446725037893782E-9 0 1 0 0 1 14 A
74 chromosome 3382079 C T 0 17 100% 0 2 0 17 4.2852131239177147E-10 0 1 0 0 6 11 T
75 chromosome 3457902 C T 2 12 80% 1 1 18 22 2.9912804175827393E-6 1 1 2 0 12 0 T
76 chromosome 3460779 T C 0 24 100% 0 2 0 19 3.101005612159882E-14 0 1 0 0 14 10 C
77 chromosome 3568849 A G 1 27 93.1% 1 2 18 17 3.7914986386187776E-15 1 1 0 1 17 10 G
78 chromosome 3696168 C T 0 27 100% 0 2 0 18 5.136266628670978E-16 0 1 0 0 14 13 T
79 chromosome 3712048 T C 0 28 100% 0 2 0 20 1.3074133236616653E-16 0 1 0 0 15 13 C
80 chromosome 3739850 A G 0 19 100% 0 2 0 17 2.829233375250701E-11 0 1 0 0 6 13 G
81 chromosome 3758015 A G 0 29 100% 0 2 0 19 3.325875998788469E-17 0 1 0 0 13 16 G
82 chromosome 3841816 G A 0 20 100% 0 2 0 19 7.254444551924877E-12 0 1 0 0 11 9 A
83 chromosome 4035203 T C 0 19 100% 0 2 0 17 2.829233375250701E-11 0 1 0 0 10 9 C
84 chromosome 4145299 C T 1 27 96.43% 1 2 17 21 3.7914986386187776E-15 1 1 0 1 15 12 T
85 chromosome 4147376 C T 1 25 96.15% 1 2 15 19 5.4444426263911445E-14 1 1 1 0 19 6 T
86 chromosome 4158968 C T 0 25 100% 0 2 0 20 7.910728602448565E-15 0 1 0 0 7 18 T
87 chromosome 4212929 G T 0 17 100% 0 2 0 17 4.2852131239177147E-10 0 1 0 0 16 1 T
88 chromosome 4232753 C T 0 29 100% 0 2 0 16 3.325875998788469E-17 0 1 0 0 17 12 T
89 chromosome 4345557 T A 1 23 95.83% 1 2 15 18 7.752514030399528E-13 1 1 1 0 21 2 A
90 chromosome 4456896 G A 0 17 100% 0 2 0 18 4.2852131239177147E-10 0 1 0 0 12 5 A
91 chromosome 4501001 G A 0 34 100% 0 2 0 19 3.5145627607868225E-20 0 1 0 0 12 22 A
92 chromosome 4519053 A G 2 24 92.31% 2 2 15 19 7.622219676947252E-13 1 1 1 1 8 16 G
93 chromosome 4519433 C A 0 16 100% 0 2 0 17 1.6636709775210046E-9 0 1 0 0 5 11 A
94 chromosome 4698084 T C 4 41 91.11% 2 2 18 20 2.040655516360998E-21 1 1 3 1 15 26 C
95 chromosome 4867375 G A 0 37 97.37% 0 1 0 22 5.726948605246429E-22 0 1 0 0 0 37 A
96 chromosome 4906423 C A 0 5 83.33% 0 1 0 17 0.003968253968253951 0 1 0 0 5 0 A
97 chromosome 4929312 T G 1 18 94.74% 1 2 23 17 5.658466750501197E-10 1 1 0 1 9 9 G
98 chromosome 4951610 G A 0 49 98% 0 2 0 19 3.925014596481366E-29 0 1 0 0 19 30 A
99 chromosome 5040523 C T 3 12 80% 1 2 17 19 5.2605276309212935E-6 1 1 3 0 9 3 T
100 chromosome 5077771 G A 0 30 96.77% 0 2 0 20 8.455616946072207E-18 0 1 0 0 19 11 A
101 chromosome 5140491 G A 0 26 100% 0 2 0 16 2.016460231996677E-15 0 1 0 0 19 7 A
102 chromosome 5157810 G A 0 17 100% 0 2 0 17 4.2852131239177147E-10 0 1 0 0 10 7 A
103 pXO1 7452 C T 1 14 87.5% 1 2 15 16 1.0314760060630275E-7 1 1 1 0 9 5 T
104 pXO1 28077 G A 3 13 81.25% 1 2 17 21 1.6120971772178452E-6 1 1 0 3 3 10 A
105 pXO1 31308 A C 1 6 85.71% 1 2 16 18 0.0023310023310023167 1 1 1 0 4 2 C
106 pXO1 55873 A T 0 34 100% 0 1 0 22 3.5145627607868225E-20 0 1 0 0 0 34 T
107 pXO1 55874 A T 0 40 100% 0 2 0 21 9.301701828018192E-24 0 1 0 0 1 39 T
108 pXO1 77518 A G 0 23 82.14% 0 2 0 18 1.214560531429256E-13 0 1 0 0 8 15 G
109 pXO1 141921 T G 1 20 95.24% 1 2 17 17 4.087260223157705E-11 1 1 1 0 7 13 G
110 pXO1 141922 T A 1 35 94.59% 1 2 21 19 8.361344963659992E-20 1 1 1 0 10 25 A
111 pXO1 141923 T A 1 52 96.3% 1 2 15 22 8.6089731799244E-30 1 1 1 0 18 34 A
112 pXO1 150892 C A 0 87 100% 0 2 0 19 6.914158005458386E-52 0 1 0 0 24 63 A