Mercurial > repos > iuc > sonneityping
diff test-data/SRR6114360.json @ 0:db4fe7172114 draft
"planemo upload for repository https://github.com/katholt/sonneityping commit 1b4231e8f98a234c29f57fef400f58f14645dc95"
| author | iuc |
|---|---|
| date | Thu, 16 Sep 2021 06:52:18 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SRR6114360.json Thu Sep 16 06:52:18 2021 +0000 @@ -0,0 +1,223 @@ +{ + "SRR6114360": { + "susceptibility": { + "quinolones": { + "predict": "S" + } + }, + "phylogenetics": { + "phylo_group": { + "Ecoli_Shigella": { + "percent_coverage": 100.0, + "median_depth": 26 + } + }, + "sub_complex": { + "Unknown": { + "percent_coverage": -1, + "median_depth": -1 + } + }, + "species": { + "Shigella_sonnei": { + "percent_coverage": 95.163, + "median_depth": 22.0 + } + }, + "lineage": { + "lineage": [ + "lineage3.7.30.4" + ], + "calls_summary": { + "lineage3.7.30.4": { + "good_nodes": 4, + "tree_depth": 4, + "genotypes": { + "lineage3": 1, + "lineage3.7": 1, + "lineage3.7.30": 1, + "lineage3.7.30.4": 1 + } + } + }, + "calls": { + "lineage3.7.30.4": { + "lineage3": { + "C59602T": { + "variant": "ref-C59602T?var_name=C59602T&num_alts=1&ref=NC_016822&enum=0&gene=NA&mut=C59602T", + "genotype": [ + 1, + 1 + ], + "genotype_likelihoods": [ + -3282.0148702940733, + -99999999, + -19.32539954665346 + ], + "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": 27, + "min_non_zero_depth": 26, + "kmer_count": 541, + "klen": 21 + } + }, + "expected_depths": [ + 26 + ], + "contamination_depths": [], + "filter": [], + "conf": 3263 + }, + "_cls": "Call.VariantCall" + } + }, + "lineage3.7": { + "G4080478A": { + "variant": "ref-G4080478A?var_name=G4080478A&num_alts=1&ref=NC_016822&enum=0&gene=NA&mut=G4080478A", + "genotype": [ + 1, + 1 + ], + "genotype_likelihoods": [ + -3961.55750528479, + -99999999, + -39.85243726626552 + ], + "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": 34, + "min_non_zero_depth": 34, + "kmer_count": 702, + "klen": 21 + } + }, + "expected_depths": [ + 26 + ], + "contamination_depths": [], + "filter": [], + "conf": 3922 + }, + "_cls": "Call.VariantCall" + } + }, + "lineage3.7.30": { + "A1138004G": { + "variant": "ref-A1138004G?var_name=A1138004G&num_alts=2&ref=NC_016822&enum=0&gene=NA&mut=A1138004G", + "genotype": [ + 1, + 1 + ], + "genotype_likelihoods": [ + -1607.6280372631725, + -99999999, + -477.52941234336663 + ], + "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": 1, + "min_non_zero_depth": 1, + "kmer_count": 20, + "klen": 21 + } + }, + "expected_depths": [ + 26 + ], + "contamination_depths": [], + "filter": [ + "LOW_TOTAL_DEPTH" + ], + "conf": 1130 + }, + "_cls": "Call.VariantCall" + } + }, + "lineage3.7.30.4": { + "G3082193A": { + "variant": "ref-G3082193A?var_name=G3082193A&num_alts=1&ref=NC_016822&enum=0&gene=NA&mut=G3082193A", + "genotype": [ + 1, + 1 + ], + "genotype_likelihoods": [ + -2726.2314885023525, + -99999999, + -40.69232343956539 + ], + "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": 20, + "min_non_zero_depth": 18, + "kmer_count": 400, + "klen": 21 + } + }, + "expected_depths": [ + 26 + ], + "contamination_depths": [], + "filter": [], + "conf": 2686 + }, + "_cls": "Call.VariantCall" + } + } + } + } + } + }, + "kmer": 21, + "probe_sets": [ + "/home/eric/miniconda3/lib/python3.8/site-packages/mykrobe/data/sonnei/sonnei.lineage.20210201.probes.fa.gz", + "/home/eric/miniconda3/lib/python3.8/site-packages/mykrobe/data/sonnei/sonnei.mlst.20201010.sonnei.fa.gz", + "/home/eric/miniconda3/lib/python3.8/site-packages/mykrobe/data/sonnei/sonnei.probe.uidA.20201010.fa.gz", + "/home/eric/miniconda3/lib/python3.8/site-packages/mykrobe/data/sonnei/sonnei.qrdr.20201010.probes.fa.gz" + ], + "files": [ + "SRR6114360_1" + ], + "version": { + "mykrobe-predictor": "v0.10.0", + "mykrobe-atlas": "v0.10.0" + }, + "genotype_model": "kmer_count" + } +} \ No newline at end of file