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comparison test-data/prediction_2020/data/ERR125628_MBOV.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 "ERR125628_MBOV": {
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_H57D-GTG2289071GTC": {
29 "variant": null,
30 "genotype": [
31 1,
32 1
33 ],
34 "genotype_likelihoods": [
35 -5562.061052007205,
36 -99999999,
37 -89.506424216315
38 ],
39 "info": {
40 "coverage": {
41 "reference": {
42 "percent_coverage": 5.0,
43 "median_depth": 0,
44 "min_non_zero_depth": 44,
45 "kmer_count": 44,
46 "klen": 21
47 },
48 "alternate": {
49 "percent_coverage": 100.0,
50 "median_depth": 46,
51 "min_non_zero_depth": 44,
52 "kmer_count": 837,
53 "klen": 19
54 }
55 },
56 "expected_depths": [
57 56.0
58 ],
59 "contamination_depths": [],
60 "filter": [],
61 "conf": 5473
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": 99.425,
81 "median_depth": 56.0
82 }
83 },
84 "sub_complex": {
85 "Unknown": {
86 "percent_coverage": -1,
87 "median_depth": -1
88 }
89 },
90 "species": {
91 "Mycobacterium_bovis": {
92 "percent_coverage": 65.402,
93 "median_depth": 48.0
94 }
95 },
96 "lineage": {
97 "lineage": [
98 "lineageBovis"
99 ],
100 "calls_summary": {
101 "lineageBovis": {
102 "good_nodes": 1,
103 "tree_depth": 1,
104 "genotypes": {
105 "lineageBovis": 1
106 }
107 }
108 },
109 "calls": {
110 "lineageBovis": {
111 "lineageBovis": {
112 "C1492605T": {
113 "variant": "ref-C1492605T?var_name=C1492605T&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=C1492605T",
114 "genotype": [
115 1,
116 1
117 ],
118 "genotype_likelihoods": [
119 -7771.156050282547,
120 -99999999,
121 -102.4977035173431
122 ],
123 "info": {
124 "coverage": {
125 "reference": {
126 "percent_coverage": 60.0,
127 "median_depth": 1,
128 "min_non_zero_depth": 1,
129 "kmer_count": 12,
130 "klen": 21
131 },
132 "alternate": {
133 "percent_coverage": 100.0,
134 "median_depth": 82,
135 "min_non_zero_depth": 75,
136 "kmer_count": 1670,
137 "klen": 21
138 }
139 },
140 "expected_depths": [
141 56.0
142 ],
143 "contamination_depths": [],
144 "filter": [],
145 "conf": 7669
146 },
147 "_cls": "Call.VariantCall"
148 }
149 }
150 }
151 }
152 }
153 },
154 "kmer": 21,
155 "probe_sets": [
156 "tb-species-170421.fasta.gz",
157 "tb-hunt-probe-set-jan-03-2019.fasta.gz",
158 "tb.lineage.20200930.probes.fa.gz"
159 ],
160 "files": [
161 "ERR125628_1.fastq",
162 "ERR125628_2.fastq"
163 ],
164 "version": {
165 "mykrobe-predictor": "v0.10.0",
166 "mykrobe-atlas": "v0.10.0"
167 },
168 "genotype_model": "kmer_count"
169 }
170 }