Mercurial > repos > iuc > hamronize_summarize
comparison test-data/mykrobe/mykrobe.json @ 5:88045b4d5597 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
author | iuc |
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date | Tue, 05 Mar 2024 19:47:21 +0000 |
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4:f8bcc852f6b3 | 5:88045b4d5597 |
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1 { | |
2 "SRR6916544": { | |
3 "susceptibility": { | |
4 "Rifampicin": { | |
5 "predict": "r", | |
6 "called_by": { | |
7 "rpoB_S450L-TCG761154TTG": { | |
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23 "min_non_zero_depth": 32, | |
24 "kmer_count": 796, | |
25 "klen": 21 | |
26 }, | |
27 "alternate": { | |
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29 "median_depth": 60, | |
30 "min_non_zero_depth": 58, | |
31 "kmer_count": 1150, | |
32 "klen": 20 | |
33 } | |
34 }, | |
35 "expected_depths": [ | |
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37 ], | |
38 "contamination_depths": [], | |
39 "filter": [], | |
40 "conf": 3458 | |
41 }, | |
42 "_cls": "Call.VariantCall" | |
43 } | |
44 } | |
45 } | |
46 }, | |
47 "phylogenetics": { | |
48 "phylo_group": { | |
49 "Mycobacterium_tuberculosis_complex": { | |
50 "percent_coverage": 99.681, | |
51 "median_depth": 124 | |
52 } | |
53 }, | |
54 "sub_complex": { | |
55 "Unknown": { | |
56 "percent_coverage": -1, | |
57 "median_depth": -1 | |
58 } | |
59 }, | |
60 "species": { | |
61 "Mycobacterium_tuberculosis": { | |
62 "percent_coverage": 98.804, | |
63 "median_depth": 121 | |
64 } | |
65 }, | |
66 "lineage": { | |
67 "lineage": [ | |
68 "lineage2.2.10", | |
69 "lineage3" | |
70 ], | |
71 "calls_summary": { | |
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74 "tree_depth": 3, | |
75 "genotypes": { | |
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77 "lineage2.2": 0.5, | |
78 "lineage2.2.10": 0.5 | |
79 } | |
80 }, | |
81 "lineage3": { | |
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84 "genotypes": { | |
85 "lineage3": 0.5 | |
86 } | |
87 } | |
88 }, | |
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107 "median_depth": 76, | |
108 "min_non_zero_depth": 70, | |
109 "kmer_count": 1498, | |
110 "klen": 21 | |
111 }, | |
112 "alternate": { | |
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114 "median_depth": 85, | |
115 "min_non_zero_depth": 82, | |
116 "kmer_count": 1695, | |
117 "klen": 21 | |
118 } | |
119 }, | |
120 "expected_depths": [ | |
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122 ], | |
123 "contamination_depths": [], | |
124 "filter": [], | |
125 "conf": 4784 | |
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127 "_cls": "Call.VariantCall" | |
128 } | |
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157 } | |
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165 }, | |
166 "_cls": "Call.VariantCall" | |
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193 "min_non_zero_depth": 42, | |
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196 } | |
197 }, | |
198 "expected_depths": [ | |
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200 ], | |
201 "contamination_depths": [], | |
202 "filter": [], | |
203 "conf": 2215 | |
204 }, | |
205 "_cls": "Call.VariantCall" | |
206 } | |
207 } | |
208 }, | |
209 "lineage3": { | |
210 "lineage3": { | |
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212 "variant": "ref-C3273107A?var_name=C3273107A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=C3273107A", | |
213 "genotype": [ | |
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217 "genotype_likelihoods": [ | |
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222 "info": { | |
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225 "percent_coverage": 100.0, | |
226 "median_depth": 66, | |
227 "min_non_zero_depth": 64, | |
228 "kmer_count": 1323, | |
229 "klen": 21 | |
230 }, | |
231 "alternate": { | |
232 "percent_coverage": 100.0, | |
233 "median_depth": 58, | |
234 "min_non_zero_depth": 54, | |
235 "kmer_count": 1160, | |
236 "klen": 21 | |
237 } | |
238 }, | |
239 "expected_depths": [ | |
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241 ], | |
242 "contamination_depths": [], | |
243 "filter": [], | |
244 "conf": 3074 | |
245 }, | |
246 "_cls": "Call.VariantCall" | |
247 } | |
248 } | |
249 } | |
250 } | |
251 } | |
252 }, | |
253 "kmer": 21, | |
254 "probe_sets": [ | |
255 "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb-species-170421.fasta.gz", | |
256 "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb-hunt-probe-set-jan-03-2019.fasta.gz", | |
257 "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb.lineage.20200930.probes.fa.gz" | |
258 ], | |
259 "files": [ | |
260 "../SRR6916544_1.fastq.gz", | |
261 "../SRR6916544_2.fastq.gz" | |
262 ], | |
263 "version": { | |
264 "mykrobe-predictor": "v0.10.0", | |
265 "mykrobe-atlas": "v0.10.0" | |
266 }, | |
267 "genotype_model": "kmer_count" | |
268 } | |
269 } |