Mercurial > repos > nml > mykrobe_parser

comparison test-data/prediction_2020/data/ERR234162_L3.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 "ERR234162_L3": {
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": 99.797,
42 "median_depth": 157.0
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": 99.33,
54 "median_depth": 142.0
55 }
56 },
57 "lineage": {
58 "lineage": [
59 "lineage3.1.1"
60 ],
61 "calls_summary": {
62 "lineage3.1.1": {
63 "good_nodes": 2,
64 "tree_depth": 3,
65 "genotypes": {
66 "lineage3": 1,
67 "lineage3.1": 0,
68 "lineage3.1.1": 1
69 }
70 }
71 },
72 "calls": {
73 "lineage3.1.1": {
74 "lineage3": {
75 "C3273107A": {
76 "variant": "ref-C3273107A?var_name=C3273107A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=C3273107A",
77 "genotype": [
78 1,
79 1
80 ],
81 "genotype_likelihoods": [
82 -22459.780019127742,
83 -99999999,
84 -183.28823056990717
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": 196,
98 "min_non_zero_depth": 190,
99 "kmer_count": 3895,
100 "klen": 21
101 }
102 },
103 "expected_depths": [
104 157.0
105 ],
106 "contamination_depths": [],
107 "filter": [],
108 "conf": 22276
109 },
110 "_cls": "Call.VariantCall"
111 }
112 },
113 "lineage3.1": null,
114 "lineage3.1.1": {
115 "G1084911A": {
116 "variant": "ref-G1084911A?var_name=G1084911A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G1084911A",
117 "genotype": [
118 1,
119 1
120 ],
121 "genotype_likelihoods": [
122 -18914.2001312626,
123 -99999999,
124 -142.3141204554317
125 ],
126 "info": {
127 "coverage": {
128 "reference": {
129 "percent_coverage": 0.0,
130 "median_depth": 0,
131 "min_non_zero_depth": 0,
132 "kmer_count": 0,
133 "klen": 21
134 },
135 "alternate": {
136 "percent_coverage": 100.0,
137 "median_depth": 149,
138 "min_non_zero_depth": 145,
139 "kmer_count": 3039,
140 "klen": 21
141 }
142 },
143 "expected_depths": [
144 157.0
145 ],
146 "contamination_depths": [],
147 "filter": [],
148 "conf": 18772
149 },
150 "_cls": "Call.VariantCall"
151 }
152 }
153 }
154 }
155 }
156 },
157 "kmer": 21,
158 "probe_sets": [
159 "tb-species-170421.fasta.gz",
160 "tb-hunt-probe-set-jan-03-2019.fasta.gz",
161 "tb.lineage.20200930.probes.fa.gz"
162 ],
163 "files": [
164 "ERR234162_1.fastq",
165 "ERR234162_2.fastq"
166 ],
167 "version": {
168 "mykrobe-predictor": "v0.10.0",
169 "mykrobe-atlas": "v0.10.0"
170 },
171 "genotype_model": "kmer_count"
172 }
173 }