Mercurial > repos > iuc > sonneityping
view 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 |
line wrap: on
line source
{ "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" } }