Mercurial > repos > nml > mykrobe_parser
diff test-data/prediction_2020/data/SRR17089001.json @ 6:8e7e5a660942 draft
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
author | nml |
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date | Fri, 22 Sep 2023 17:24:02 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prediction_2020/data/SRR17089001.json Fri Sep 22 17:24:02 2023 +0000 @@ -0,0 +1,131 @@ +{ + "SRR17089001": { + "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": 99.448, + "median_depth": 240.0 + } + }, + "sub_complex": { + "Unknown": { + "percent_coverage": -1, + "median_depth": -1 + } + }, + "species": { + "Mycobacterium_africanum": { + "percent_coverage": 54.809, + "median_depth": 263 + } + }, + "lineage": { + "lineage": [ + "clade_animal_A3" + ], + "calls_summary": { + "clade_animal_A3": { + "good_nodes": 1, + "tree_depth": 1, + "genotypes": { + "clade_animal_A3": 1 + } + } + }, + "calls": { + "clade_animal_A3": { + "clade_animal_A3": { + "T154276G": { + "variant": "ref-T154276G?var_name=T154276G&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=T154276G", + "genotype": [ + 1, + 1 + ], + "genotype_likelihoods": [ + -28853.072634655364, + -99999999, + -233.08196525549602 + ], + "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": 231, + "min_non_zero_depth": 227, + "kmer_count": 4627, + "klen": 21 + } + }, + "expected_depths": [ + 240.0 + ], + "contamination_depths": [], + "filter": [], + "conf": 28620 + }, + "_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": [ + "SRR17089001_1.fastq", + "SRR17089001_2.fastq" + ], + "version": { + "mykrobe-predictor": "v0.10.0", + "mykrobe-atlas": "v0.10.0" + }, + "genotype_model": "kmer_count" + } +}