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comparison test-data/prediction_2019/data/ERR2704812_L5.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 "ERR2704812_L5": {
3 "susceptibility": {
4 "Ofloxacin": {
5 "predict": "S"
6 },
7 "Moxifloxacin": {
8 "predict": "S"
9 },
10 "Isoniazid": {
11 "predict": "R",
12 "called_by": {
13 "ahpC_G-48A-G2726145A": {
14 "variant": null,
15 "genotype": [
16 1,
17 1
18 ],
19 "genotype_likelihoods": [
20 -43297.59603037145,
21 -99999999,
22 -315.05757839655627
23 ],
24 "info": {
25 "coverage": {
26 "reference": {
27 "percent_coverage": 0.0,
28 "median_depth": 0,
29 "min_non_zero_depth": 0,
30 "kmer_count": 0,
31 "klen": 21
32 },
33 "alternate": {
34 "percent_coverage": 100.0,
35 "median_depth": 360,
36 "min_non_zero_depth": 352,
37 "kmer_count": 7229,
38 "klen": 21
39 }
40 },
41 "expected_depths": [
42 332.0
43 ],
44 "contamination_depths": [],
45 "filter": [],
46 "conf": 42983
47 },
48 "_cls": "Call.VariantCall"
49 }
50 }
51 },
52 "Kanamycin": {
53 "predict": "S"
54 },
55 "Ethambutol": {
56 "predict": "S"
57 },
58 "Streptomycin": {
59 "predict": "S"
60 },
61 "Ciprofloxacin": {
62 "predict": "S"
63 },
64 "Pyrazinamide": {
65 "predict": "S"
66 },
67 "Rifampicin": {
68 "predict": "R",
69 "called_by": {
70 "rpoB_D435V-GAC761109GTC": {
71 "variant": null,
72 "genotype": [
73 1,
74 1
75 ],
76 "genotype_likelihoods": [
77 -40815.43149991495,
78 -99999999,
79 -318.2103823437153
80 ],
81 "info": {
82 "coverage": {
83 "reference": {
84 "percent_coverage": 0.0,
85 "median_depth": 0,
86 "min_non_zero_depth": 0,
87 "kmer_count": 0,
88 "klen": 21
89 },
90 "alternate": {
91 "percent_coverage": 100.0,
92 "median_depth": 344,
93 "min_non_zero_depth": 328,
94 "kmer_count": 6544,
95 "klen": 20
96 }
97 },
98 "expected_depths": [
99 332.0
100 ],
101 "contamination_depths": [],
102 "filter": [],
103 "conf": 40497
104 },
105 "_cls": "Call.VariantCall"
106 }
107 }
108 },
109 "Amikacin": {
110 "predict": "S"
111 },
112 "Capreomycin": {
113 "predict": "S"
114 }
115 },
116 "phylogenetics": {
117 "phylo_group": {
118 "Mycobacterium_tuberculosis_complex": {
119 "percent_coverage": 98.467,
120 "median_depth": 332.0
121 }
122 },
123 "sub_complex": {
124 "Unknown": {
125 "percent_coverage": -1,
126 "median_depth": -1
127 }
128 },
129 "species": {
130 "Mycobacterium_africanum": {
131 "percent_coverage": 64.333,
132 "median_depth": 326
133 }
134 },
135 "lineage": {
136 "Unknown": {
137 "percent_coverage": -1,
138 "median_depth": -1
139 }
140 }
141 },
142 "kmer": 21,
143 "probe_sets": [
144 "tb-species-170421.fasta.gz",
145 "tb-hunt-probe-set-jan-03-2019.fasta.gz"
146 ],
147 "files": [
148 "ERR2704812_1.fastq",
149 "ERR2704812_2.fastq"
150 ],
151 "version": {
152 "mykrobe-predictor": "v0.10.0",
153 "mykrobe-atlas": "v0.10.0"
154 },
155 "genotype_model": "kmer_count"
156 }
157 }