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comparison test-data/prediction_2019/data/ERR3335753_L1.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 "ERR3335753_L1": {
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_T389TG-A2288853CA": {
29 "variant": null,
30 "genotype": [
31 0,
32 1
33 ],
34 "genotype_likelihoods": [
35 -1707.2912821258215,
36 -685.0256738025864,
37 -10049.785656880731
38 ],
39 "info": {
40 "coverage": {
41 "reference": {
42 "percent_coverage": 100.0,
43 "median_depth": 131,
44 "min_non_zero_depth": 128,
45 "kmer_count": 2768,
46 "klen": 21
47 },
48 "alternate": {
49 "percent_coverage": 100.0,
50 "median_depth": 43,
51 "min_non_zero_depth": 41,
52 "kmer_count": 779,
53 "klen": 19
54 }
55 },
56 "expected_depths": [
57 236.0
58 ],
59 "contamination_depths": [],
60 "filter": [],
61 "conf": 1022
62 },
63 "_cls": "Call.VariantCall"
64 },
65 "pncA_G390GG-C2288852CC": {
66 "variant": null,
67 "genotype": [
68 0,
69 1
70 ],
71 "genotype_likelihoods": [
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75 ],
76 "info": {
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80 "median_depth": 130,
81 "min_non_zero_depth": 128,
82 "kmer_count": 2719,
83 "klen": 21
84 },
85 "alternate": {
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87 "median_depth": 43,
88 "min_non_zero_depth": 41,
89 "kmer_count": 779,
90 "klen": 19
91 }
92 },
93 "expected_depths": [
94 236.0
95 ],
96 "contamination_depths": [],
97 "filter": [],
98 "conf": 1055
99 },
100 "_cls": "Call.VariantCall"
101 },
102 "pncA_G391GG-C2288851CC": {
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104 "genotype": [
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106 1
107 ],
108 "genotype_likelihoods": [
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111 -9858.860191248112
112 ],
113 "info": {
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117 "median_depth": 130,
118 "min_non_zero_depth": 128,
119 "kmer_count": 2715,
120 "klen": 21
121 },
122 "alternate": {
123 "percent_coverage": 100.0,
124 "median_depth": 43,
125 "min_non_zero_depth": 41,
126 "kmer_count": 779,
127 "klen": 19
128 }
129 },
130 "expected_depths": [
131 236.0
132 ],
133 "contamination_depths": [],
134 "filter": [],
135 "conf": 1058
136 },
137 "_cls": "Call.VariantCall"
138 }
139 }
140 },
141 "Rifampicin": {
142 "predict": "R",
143 "called_by": {
144 "rpoB_L430P-CTG761094CCG": {
145 "variant": null,
146 "genotype": [
147 1,
148 1
149 ],
150 "genotype_likelihoods": [
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152 -2370.6712704022216,
153 -210.1929350878079
154 ],
155 "info": {
156 "coverage": {
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159 "median_depth": 5,
160 "min_non_zero_depth": 3,
161 "kmer_count": 101,
162 "klen": 21
163 },
164 "alternate": {
165 "percent_coverage": 100.0,
166 "median_depth": 190,
167 "min_non_zero_depth": 188,
168 "kmer_count": 3622,
169 "klen": 20
170 }
171 },
172 "expected_depths": [
173 236.0
174 ],
175 "contamination_depths": [],
176 "filter": [],
177 "conf": 14588
178 },
179 "_cls": "Call.VariantCall"
180 }
181 }
182 },
183 "Amikacin": {
184 "predict": "S"
185 },
186 "Capreomycin": {
187 "predict": "S"
188 }
189 },
190 "phylogenetics": {
191 "phylo_group": {
192 "Mycobacterium_tuberculosis_complex": {
193 "percent_coverage": 99.69,
194 "median_depth": 236.0
195 }
196 },
197 "sub_complex": {
198 "Unknown": {
199 "percent_coverage": -1,
200 "median_depth": -1
201 }
202 },
203 "species": {
204 "Mycobacterium_tuberculosis": {
205 "percent_coverage": 98.335,
206 "median_depth": 220
207 }
208 },
209 "lineage": {
210 "East_Africa_Indian_ocean": {
211 "percent_coverage": 100.0,
212 "median_depth": 193
213 }
214 }
215 },
216 "kmer": 21,
217 "probe_sets": [
218 "tb-species-170421.fasta.gz",
219 "tb-hunt-probe-set-jan-03-2019.fasta.gz"
220 ],
221 "files": [
222 "ERR3335753_1.fastq",
223 "ERR3335753_2.fastq"
224 ],
225 "version": {
226 "mykrobe-predictor": "v0.10.0",
227 "mykrobe-atlas": "v0.10.0"
228 },
229 "genotype_model": "kmer_count"
230 }
231 }