annotate test-data/prediction_2019/data/ERR3335753_L1.json @ 6:8e7e5a660942 draft

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

{
    "ERR3335753_L1": {
        "susceptibility": {
            "Ofloxacin": {
                "predict": "S"
            },
            "Moxifloxacin": {
                "predict": "S"
            },
            "Isoniazid": {
                "predict": "S"
            },
            "Kanamycin": {
                "predict": "S"
            },
            "Ethambutol": {
                "predict": "S"
            },
            "Streptomycin": {
                "predict": "S"
            },
            "Ciprofloxacin": {
                "predict": "S"
            },
            "Pyrazinamide": {
                "predict": "r",
                "called_by": {
                    "pncA_T389TG-A2288853CA": {
                        "variant": null,
                        "genotype": [
                            0,
                            1
                        ],
                        "genotype_likelihoods": [
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                            -685.0256738025864,
                            -10049.785656880731
                        ],
                        "info": {
                            "coverage": {
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                                    "percent_coverage": 100.0,
                                    "median_depth": 131,
                                    "min_non_zero_depth": 128,
                                    "kmer_count": 2768,
                                    "klen": 21
                                },
                                "alternate": {
                                    "percent_coverage": 100.0,
                                    "median_depth": 43,
                                    "min_non_zero_depth": 41,
                                    "kmer_count": 779,
                                    "klen": 19
                                }
                            },
                            "expected_depths": [
                                236.0
                            ],
                            "contamination_depths": [],
                            "filter": [],
                            "conf": 1022
                        },
                        "_cls": "Call.VariantCall"
                    },
                    "pncA_G390GG-C2288852CC": {
                        "variant": null,
                        "genotype": [
                            0,
                            1
                        ],
                        "genotype_likelihoods": [
                            -1736.2599622230955,
                            -680.8401734761619,
                            -9873.233821297094
                        ],
                        "info": {
                            "coverage": {
                                "reference": {
                                    "percent_coverage": 100.0,
                                    "median_depth": 130,
                                    "min_non_zero_depth": 128,
                                    "kmer_count": 2719,
                                    "klen": 21
                                },
                                "alternate": {
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                                    "median_depth": 43,
                                    "min_non_zero_depth": 41,
                                    "kmer_count": 779,
                                    "klen": 19
                                }
                            },
                            "expected_depths": [
                                236.0
                            ],
                            "contamination_depths": [],
                            "filter": [],
                            "conf": 1055
                        },
                        "_cls": "Call.VariantCall"
                    },
                    "pncA_G391GG-C2288851CC": {
                        "variant": null,
                        "genotype": [
                            0,
                            1
                        ],
                        "genotype_likelihoods": [
                            -1738.6635171276575,
                            -680.5372646726655,
                            -9858.860191248112
                        ],
                        "info": {
                            "coverage": {
                                "reference": {
                                    "percent_coverage": 100.0,
                                    "median_depth": 130,
                                    "min_non_zero_depth": 128,
                                    "kmer_count": 2715,
                                    "klen": 21
                                },
                                "alternate": {
                                    "percent_coverage": 100.0,
                                    "median_depth": 43,
                                    "min_non_zero_depth": 41,
                                    "kmer_count": 779,
                                    "klen": 19
                                }
                            },
                            "expected_depths": [
                                236.0
                            ],
                            "contamination_depths": [],
                            "filter": [],
                            "conf": 1058
                        },
                        "_cls": "Call.VariantCall"
                    }
                }
            },
            "Rifampicin": {
                "predict": "R",
                "called_by": {
                    "rpoB_L430P-CTG761094CCG": {
                        "variant": null,
                        "genotype": [
                            1,
                            1
                        ],
                        "genotype_likelihoods": [
                            -14797.71027662235,
                            -2370.6712704022216,
                            -210.1929350878079
                        ],
                        "info": {
                            "coverage": {
                                "reference": {
                                    "percent_coverage": 100.0,
                                    "median_depth": 5,
                                    "min_non_zero_depth": 3,
                                    "kmer_count": 101,
                                    "klen": 21
                                },
                                "alternate": {
                                    "percent_coverage": 100.0,
                                    "median_depth": 190,
                                    "min_non_zero_depth": 188,
                                    "kmer_count": 3622,
                                    "klen": 20
                                }
                            },
                            "expected_depths": [
                                236.0
                            ],
                            "contamination_depths": [],
                            "filter": [],
                            "conf": 14588
                        },
                        "_cls": "Call.VariantCall"
                    }
                }
            },
            "Amikacin": {
                "predict": "S"
            },
            "Capreomycin": {
                "predict": "S"
            }
        },
        "phylogenetics": {
            "phylo_group": {
                "Mycobacterium_tuberculosis_complex": {
                    "percent_coverage": 99.69,
                    "median_depth": 236.0
                }
            },
            "sub_complex": {
                "Unknown": {
                    "percent_coverage": -1,
                    "median_depth": -1
                }
            },
            "species": {
                "Mycobacterium_tuberculosis": {
                    "percent_coverage": 98.335,
                    "median_depth": 220
                }
            },
            "lineage": {
                "East_Africa_Indian_ocean": {
                    "percent_coverage": 100.0,
                    "median_depth": 193
                }
            }
        },
        "kmer": 21,
        "probe_sets": [
            "tb-species-170421.fasta.gz",
            "tb-hunt-probe-set-jan-03-2019.fasta.gz"
        ],
        "files": [
            "ERR3335753_1.fastq",
            "ERR3335753_2.fastq"
        ],
        "version": {
            "mykrobe-predictor": "v0.10.0",
            "mykrobe-atlas": "v0.10.0"
        },
        "genotype_model": "kmer_count"
    }
}