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comparison test-data/prediction_2019/data/ERR266106_MCAN.json @ 6:8e7e5a660942 draft

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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
author nml
date Fri, 22 Sep 2023 17:24:02 +0000
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5:deebc6410d13 6:8e7e5a660942
1 {
2 "ERR266106_MCAN": {
3 "susceptibility": {
4 "Ofloxacin": {
5 "predict": "S"
6 },
7 "Moxifloxacin": {
8 "predict": "S"
9 },
10 "Isoniazid": {
11 "predict": "S"
12 },
13 "Kanamycin": {
14 "predict": "S"
15 },
16 "Ethambutol": {
17 "predict": "S"
18 },
19 "Streptomycin": {
20 "predict": "S"
21 },
22 "Ciprofloxacin": {
23 "predict": "S"
24 },
25 "Pyrazinamide": {
26 "predict": "R",
27 "called_by": {
28 "pncA_GCA136GCG-TGC2289104CGC": {
29 "variant": null,
30 "genotype": [
31 1,
32 1
33 ],
34 "genotype_likelihoods": [
35 -12364.590650703674,
36 -99999999,
37 -79.29166435006414
38 ],
39 "info": {
40 "coverage": {
41 "reference": {
42 "percent_coverage": 0.0,
43 "median_depth": 0,
44 "min_non_zero_depth": 0,
45 "kmer_count": 0,
46 "klen": 21
47 },
48 "alternate": {
49 "percent_coverage": 100.0,
50 "median_depth": 100,
51 "min_non_zero_depth": 92,
52 "kmer_count": 2016,
53 "klen": 21
54 }
55 },
56 "expected_depths": [
57 100
58 ],
59 "contamination_depths": [],
60 "filter": [],
61 "conf": 12285
62 },
63 "_cls": "Call.VariantCall"
64 }
65 }
66 },
67 "Rifampicin": {
68 "predict": "S"
69 },
70 "Amikacin": {
71 "predict": "S"
72 },
73 "Capreomycin": {
74 "predict": "S"
75 }
76 },
77 "phylogenetics": {
78 "phylo_group": {
79 "Mycobacterium_tuberculosis_complex": {
80 "percent_coverage": 98.352,
81 "median_depth": 100
82 }
83 },
84 "sub_complex": {
85 "Unknown": {
86 "percent_coverage": -1,
87 "median_depth": -1
88 }
89 },
90 "species": {
91 "Mycobacterium_tuberculosis": {
92 "percent_coverage": 73.899,
93 "median_depth": 92.0
94 }
95 },
96 "lineage": {
97 "Mycobacterium_tuberculosis_subsp_canettii": {
98 "percent_coverage": 63.718,
99 "median_depth": 94.0
100 }
101 }
102 },
103 "kmer": 21,
104 "probe_sets": [
105 "tb-species-170421.fasta.gz",
106 "tb-hunt-probe-set-jan-03-2019.fasta.gz"
107 ],
108 "files": [
109 "ERR266106_1.fastq",
110 "ERR266106_2.fastq"
111 ],
112 "version": {
113 "mykrobe-predictor": "v0.10.0",
114 "mykrobe-atlas": "v0.10.0"
115 },
116 "genotype_model": "kmer_count"
117 }
118 }