Mercurial > repos > nml > mykrobe_parser
diff test-data/prediction_2020/data/ERR234162_L3.json @ 6:8e7e5a660942 draft
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
| author | nml |
|---|---|
| date | Fri, 22 Sep 2023 17:24:02 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prediction_2020/data/ERR234162_L3.json Fri Sep 22 17:24:02 2023 +0000 @@ -0,0 +1,173 @@ +{ + "ERR234162_L3": { + "susceptibility": { + "Ofloxacin": { + "predict": "S" + }, + "Moxifloxacin": { + "predict": "S" + }, + "Isoniazid": { + "predict": "S" + }, + "Kanamycin": { + "predict": "S" + }, + "Ethambutol": { + "predict": "S" + }, + "Streptomycin": { + "predict": "S" + }, + "Ciprofloxacin": { + "predict": "S" + }, + "Pyrazinamide": { + "predict": "S" + }, + "Rifampicin": { + "predict": "S" + }, + "Amikacin": { + "predict": "S" + }, + "Capreomycin": { + "predict": "S" + } + }, + "phylogenetics": { + "phylo_group": { + "Mycobacterium_tuberculosis_complex": { + "percent_coverage": 99.797, + "median_depth": 157.0 + } + }, + "sub_complex": { + "Unknown": { + "percent_coverage": -1, + "median_depth": -1 + } + }, + "species": { + "Mycobacterium_tuberculosis": { + "percent_coverage": 99.33, + "median_depth": 142.0 + } + }, + "lineage": { + "lineage": [ + "lineage3.1.1" + ], + "calls_summary": { + "lineage3.1.1": { + "good_nodes": 2, + "tree_depth": 3, + "genotypes": { + "lineage3": 1, + "lineage3.1": 0, + "lineage3.1.1": 1 + } + } + }, + "calls": { + "lineage3.1.1": { + "lineage3": { + "C3273107A": { + "variant": "ref-C3273107A?var_name=C3273107A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=C3273107A", + "genotype": [ + 1, + 1 + ], + "genotype_likelihoods": [ + -22459.780019127742, + -99999999, + -183.28823056990717 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 0.0, + "median_depth": 0, + "min_non_zero_depth": 0, + "kmer_count": 0, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 196, + "min_non_zero_depth": 190, + "kmer_count": 3895, + "klen": 21 + } + }, + "expected_depths": [ + 157.0 + ], + "contamination_depths": [], + "filter": [], + "conf": 22276 + }, + "_cls": "Call.VariantCall" + } + }, + "lineage3.1": null, + "lineage3.1.1": { + "G1084911A": { + "variant": "ref-G1084911A?var_name=G1084911A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G1084911A", + "genotype": [ + 1, + 1 + ], + "genotype_likelihoods": [ + -18914.2001312626, + -99999999, + -142.3141204554317 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 0.0, + "median_depth": 0, + "min_non_zero_depth": 0, + "kmer_count": 0, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 149, + "min_non_zero_depth": 145, + "kmer_count": 3039, + "klen": 21 + } + }, + "expected_depths": [ + 157.0 + ], + "contamination_depths": [], + "filter": [], + "conf": 18772 + }, + "_cls": "Call.VariantCall" + } + } + } + } + } + }, + "kmer": 21, + "probe_sets": [ + "tb-species-170421.fasta.gz", + "tb-hunt-probe-set-jan-03-2019.fasta.gz", + "tb.lineage.20200930.probes.fa.gz" + ], + "files": [ + "ERR234162_1.fastq", + "ERR234162_2.fastq" + ], + "version": { + "mykrobe-predictor": "v0.10.0", + "mykrobe-atlas": "v0.10.0" + }, + "genotype_model": "kmer_count" + } +}