annotate test-data/single_2020/single2020.json @ 6:8e7e5a660942 draft

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

{
    "ERR2704812_L5": {
        "susceptibility": {
            "Ofloxacin": {
                "predict": "S"
            },
            "Moxifloxacin": {
                "predict": "S"
            },
            "Isoniazid": {
                "predict": "R",
                "called_by": {
                    "ahpC_G-48A-G2726145A": {
                        "variant": null,
                        "genotype": [
                            1,
                            1
                        ],
                        "genotype_likelihoods": [
                            -43297.59603037145,
                            -99999999,
                            -315.05757839655627
                        ],
                        "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": 360,
                                    "min_non_zero_depth": 352,
                                    "kmer_count": 7229,
                                    "klen": 21
                                }
                            },
                            "expected_depths": [
                                332.0
                            ],
                            "contamination_depths": [],
                            "filter": [],
                            "conf": 42983
                        },
                        "_cls": "Call.VariantCall"
                    }
                }
            },
            "Kanamycin": {
                "predict": "S"
            },
            "Ethambutol": {
                "predict": "S"
            },
            "Streptomycin": {
                "predict": "S"
            },
            "Ciprofloxacin": {
                "predict": "S"
            },
            "Pyrazinamide": {
                "predict": "S"
            },
            "Rifampicin": {
                "predict": "R",
                "called_by": {
                    "rpoB_D435V-GAC761109GTC": {
                        "variant": null,
                        "genotype": [
                            1,
                            1
                        ],
                        "genotype_likelihoods": [
                            -40815.43149991495,
                            -99999999,
                            -318.2103823437153
                        ],
                        "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": 344,
                                    "min_non_zero_depth": 328,
                                    "kmer_count": 6544,
                                    "klen": 20
                                }
                            },
                            "expected_depths": [
                                332.0
                            ],
                            "contamination_depths": [],
                            "filter": [],
                            "conf": 40497
                        },
                        "_cls": "Call.VariantCall"
                    }
                }
            },
            "Amikacin": {
                "predict": "S"
            },
            "Capreomycin": {
                "predict": "S"
            }
        },
        "phylogenetics": {
            "phylo_group": {
                "Mycobacterium_tuberculosis_complex": {
                    "percent_coverage": 98.467,
                    "median_depth": 332.0
                }
            },
            "sub_complex": {
                "Unknown": {
                    "percent_coverage": -1,
                    "median_depth": -1
                }
            },
            "species": {
                "Mycobacterium_africanum": {
                    "percent_coverage": 64.333,
                    "median_depth": 326
                }
            },
            "lineage": {
                "lineage": [
                    "lineage5"
                ],
                "calls_summary": {
                    "lineage5": {
                        "good_nodes": 1,
                        "tree_depth": 1,
                        "genotypes": {
                            "lineage5": 1
                        }
                    }
                },
                "calls": {
                    "lineage5": {
                        "lineage5": {
                            "C1799921A": {
                                "variant": "ref-C1799921A?var_name=C1799921A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=C1799921A",
                                "genotype": [
                                    1,
                                    1
                                ],
                                "genotype_likelihoods": [
                                    -40869.16316992115,
                                    -99999999,
                                    -318.61512332363264
                                ],
                                "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": 331,
                                            "min_non_zero_depth": 327,
                                            "kmer_count": 6635,
                                            "klen": 21
                                        }
                                    },
                                    "expected_depths": [
                                        332.0
                                    ],
                                    "contamination_depths": [],
                                    "filter": [],
                                    "conf": 40551
                                },
                                "_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": [
            "ERR2704812_1.fastq",
            "ERR2704812_2.fastq"
        ],
        "version": {
            "mykrobe-predictor": "v0.10.0",
            "mykrobe-atlas": "v0.10.0"
        },
        "genotype_model": "kmer_count"
    }
}