annotate test-data/prediction_2020/data/SRR3500411_MMUN.json @ 6:8e7e5a660942 draft

planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2

{
    "SRR3500411_MMUN": {
        "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": 99.568,
                    "median_depth": 114.0
                }
            },
            "sub_complex": {
                "Unknown": {
                    "percent_coverage": -1,
                    "median_depth": -1
                }
            },
            "species": {
                "Mycobacterium_africanum": {
                    "percent_coverage": 62.167,
                    "median_depth": 94.0
                }
            },
            "lineage": {
                "lineage": [
                    "clade_animal_A1"
                ],
                "calls_summary": {
                    "clade_animal_A1": {
                        "good_nodes": 1,
                        "tree_depth": 1,
                        "genotypes": {
                            "clade_animal_A1": 1
                        }
                    }
                },
                "calls": {
                    "clade_animal_A1": {
                        "clade_animal_A1": {
                            "G2873278T": {
                                "variant": "ref-G2873278T?var_name=G2873278T&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G2873278T",
                                "genotype": [
                                    1,
                                    1
                                ],
                                "genotype_likelihoods": [
                                    -11085.68809338619,
                                    -99999999,
                                    -274.747110554358
                                ],
                                "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": 76,
                                            "min_non_zero_depth": 71,
                                            "kmer_count": 1518,
                                            "klen": 21
                                        }
                                    },
                                    "expected_depths": [
                                        114.0
                                    ],
                                    "contamination_depths": [],
                                    "filter": [],
                                    "conf": 10811
                                },
                                "_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": [
            "SRR3500411_1.fastq",
            "SRR3500411_2.fastq"
        ],
        "version": {
            "mykrobe-predictor": "v0.10.0",
            "mykrobe-atlas": "v0.10.0"
        },
        "genotype_model": "kmer_count"
    }
}