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comparison test-data/prediction_2020/data/ERR031480_L6.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 "ERR031480_L6": {
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": "S"
27 },
28 "Rifampicin": {
29 "predict": "S"
30 },
31 "Amikacin": {
32 "predict": "S"
33 },
34 "Capreomycin": {
35 "predict": "S"
36 }
37 },
38 "phylogenetics": {
39 "phylo_group": {
40 "Mycobacterium_tuberculosis_complex": {
41 "percent_coverage": 99.776,
42 "median_depth": 136.0
43 }
44 },
45 "sub_complex": {
46 "Unknown": {
47 "percent_coverage": -1,
48 "median_depth": -1
49 }
50 },
51 "species": {
52 "Mycobacterium_africanum": {
53 "percent_coverage": 89.738,
54 "median_depth": 167
55 }
56 },
57 "lineage": {
58 "lineage": [
59 "lineage6"
60 ],
61 "calls_summary": {
62 "lineage6": {
63 "good_nodes": 1,
64 "tree_depth": 1,
65 "genotypes": {
66 "lineage6": 1
67 }
68 }
69 },
70 "calls": {
71 "lineage6": {
72 "lineage6": {
73 "C1816587G": {
74 "variant": "ref-C1816587G?var_name=C1816587G&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=C1816587G",
75 "genotype": [
76 1,
77 1
78 ],
79 "genotype_likelihoods": [
80 -10600.495296713667,
81 -1720.7989957550876,
82 -33.52511446152958
83 ],
84 "info": {
85 "coverage": {
86 "reference": {
87 "percent_coverage": 100.0,
88 "median_depth": 1,
89 "min_non_zero_depth": 1,
90 "kmer_count": 20,
91 "klen": 21
92 },
93 "alternate": {
94 "percent_coverage": 100.0,
95 "median_depth": 131,
96 "min_non_zero_depth": 122,
97 "kmer_count": 2601,
98 "klen": 21
99 }
100 },
101 "expected_depths": [
102 136.0
103 ],
104 "contamination_depths": [],
105 "filter": [],
106 "conf": 10567
107 },
108 "_cls": "Call.VariantCall"
109 }
110 }
111 }
112 }
113 }
114 },
115 "kmer": 21,
116 "probe_sets": [
117 "tb-species-170421.fasta.gz",
118 "tb-hunt-probe-set-jan-03-2019.fasta.gz",
119 "tb.lineage.20200930.probes.fa.gz"
120 ],
121 "files": [
122 "ERR031480_1.fastq",
123 "ERR031480_2.fastq"
124 ],
125 "version": {
126 "mykrobe-predictor": "v0.10.0",
127 "mykrobe-atlas": "v0.10.0"
128 },
129 "genotype_model": "kmer_count"
130 }
131 }