comparison test-data/SRR6114360.json @ 0:3a328b3aeb65 draft default tip

"planemo upload for repository https://github.com/katholt/sonneityping commit 1b4231e8f98a234c29f57fef400f58f14645dc95"

0:3a328b3aeb65

{
    "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": {
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                        "tree_depth": 4,
                        "genotypes": {
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                            "lineage3.7": 1,
                            "lineage3.7.30": 1,
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                        }
                    }
                },
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                                "genotype": [
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                                ],
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                                "info": {
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                                            "median_depth": 0,
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                                            "kmer_count": 0,
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                                            "kmer_count": 541,
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                                    "contamination_depths": [],
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                                },
                                "_cls": "Call.VariantCall"
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                        },
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                                    },
                                    "expected_depths": [
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                                    "contamination_depths": [],
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                                "_cls": "Call.VariantCall"
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                        },
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                                        },
                                        "alternate": {
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                                    "expected_depths": [
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                                    "contamination_depths": [],
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                                },
                                "_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": {
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            "mykrobe-atlas": "v0.10.0"
        },
        "genotype_model": "kmer_count"
    }
}