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comparison test-data/prediction_2020/data/SRR1710097_L2.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 "SRR1710097_L2": {
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": 99.686,
42 "median_depth": 420
43 }
44 },
45 "sub_complex": {
46 "Unknown": {
47 "percent_coverage": -1,
48 "median_depth": -1
49 }
50 },
51 "species": {
52 "Mycobacterium_tuberculosis": {
53 "percent_coverage": 98.909,
54 "median_depth": 403.0
55 }
56 },
57 "lineage": {
58 "lineage": [
59 "lineage2.2.4"
60 ],
61 "calls_summary": {
62 "lineage2.2.4": {
63 "good_nodes": 3,
64 "tree_depth": 3,
65 "genotypes": {
66 "lineage2": 1,
67 "lineage2.2": 1,
68 "lineage2.2.4": 1
69 }
70 }
71 },
72 "calls": {
73 "lineage2.2.4": {
74 "lineage2": {
75 "G497491A": {
76 "variant": "ref-G497491A?var_name=G497491A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G497491A",
77 "genotype": [
78 1,
79 1
80 ],
81 "genotype_likelihoods": [
82 -53081.870411575976,
83 -99999999,
84 -401.73206510437967
85 ],
86 "info": {
87 "coverage": {
88 "reference": {
89 "percent_coverage": 0.0,
90 "median_depth": 0,
91 "min_non_zero_depth": 0,
92 "kmer_count": 0,
93 "klen": 21
94 },
95 "alternate": {
96 "percent_coverage": 100.0,
97 "median_depth": 438,
98 "min_non_zero_depth": 424,
99 "kmer_count": 8731,
100 "klen": 21
101 }
102 },
103 "expected_depths": [
104 420
105 ],
106 "contamination_depths": [],
107 "filter": [],
108 "conf": 52680
109 },
110 "_cls": "Call.VariantCall"
111 }
112 },
113 "lineage2.2": {
114 "G2505085A": {
115 "variant": "ref-G2505085A?var_name=G2505085A&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=G2505085A",
116 "genotype": [
117 1,
118 1
119 ],
120 "genotype_likelihoods": [
121 -49633.185227023845,
122 -99999999,
123 -453.6542893522951
124 ],
125 "info": {
126 "coverage": {
127 "reference": {
128 "percent_coverage": 0.0,
129 "median_depth": 0,
130 "min_non_zero_depth": 0,
131 "kmer_count": 0,
132 "klen": 21
133 },
134 "alternate": {
135 "percent_coverage": 100.0,
136 "median_depth": 418,
137 "min_non_zero_depth": 262,
138 "kmer_count": 7876,
139 "klen": 21
140 }
141 },
142 "expected_depths": [
143 420
144 ],
145 "contamination_depths": [],
146 "filter": [],
147 "conf": 49180
148 },
149 "_cls": "Call.VariantCall"
150 }
151 },
152 "lineage2.2.4": {
153 "A782634G": {
154 "variant": "ref-A782634G?var_name=A782634G&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=A782634G",
155 "genotype": [
156 1,
157 1
158 ],
159 "genotype_likelihoods": [
160 -52377.030507181364,
161 -99999999,
162 -405.20219781199785
163 ],
164 "info": {
165 "coverage": {
166 "reference": {
167 "percent_coverage": 0.0,
168 "median_depth": 0,
169 "min_non_zero_depth": 0,
170 "kmer_count": 0,
171 "klen": 21
172 },
173 "alternate": {
174 "percent_coverage": 100.0,
175 "median_depth": 427,
176 "min_non_zero_depth": 414,
177 "kmer_count": 8558,
178 "klen": 21
179 }
180 },
181 "expected_depths": [
182 420
183 ],
184 "contamination_depths": [],
185 "filter": [],
186 "conf": 51972
187 },
188 "_cls": "Call.VariantCall"
189 }
190 }
191 }
192 }
193 }
194 },
195 "kmer": 21,
196 "probe_sets": [
197 "tb-species-170421.fasta.gz",
198 "tb-hunt-probe-set-jan-03-2019.fasta.gz",
199 "tb.lineage.20200930.probes.fa.gz"
200 ],
201 "files": [
202 "SRR1710097_1.fastq",
203 "SRR1710097_2.fastq"
204 ],
205 "version": {
206 "mykrobe-predictor": "v0.10.0",
207 "mykrobe-atlas": "v0.10.0"
208 },
209 "genotype_model": "kmer_count"
210 }
211 }