{"id":"W4322621620","doi":"10.1101/2023.02.27.530375","title":"Whole Genome Sequencing based Identification of Human Tuberculosis caused by Animal-lineage <i>Mycobacterium orygis</i>","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Provincial Laboratory of Public Health; BC Centre for Disease Control; University of Manitoba; Public Health Agency of Canada","funders":"","keywords":"Biology; Phylogenetic tree; Mycobacterium tuberculosis complex; Genetics; Single-nucleotide polymorphism; Genome; Identification (biology); Whole genome sequencing; Tuberculosis; Reference genome; Mycobacterium tuberculosis; Evolutionary biology; Genotype; Gene; Medicine; Ecology","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001766356,0.0002313665,0.0002532215,0.0006211509,0.0002960731,0.0003470415,0.0001383216,0.0002919509,0.0006349065],"category_scores_gemma":[0.00030157,0.0000860374,0.0003136912,0.0007526406,0.0001652532,0.00005883128,0.0001517411,0.0001792319,0.000196206],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003207961,"about_ca_system_score_gemma":0.0005425988,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.04074488,"about_ca_topic_score_gemma":0.05131116,"domain_scores_codex":[0.9998001,0.00002215277,0.00001586176,0.00007055602,0.00005687568,0.00003440561],"domain_scores_gemma":[0.9998473,0.00002425679,0.00004034072,0.00001338223,0.00005466654,0.00002008708],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0009482336,0.000107102,0.3334781,0.0002888856,0.0002601287,0.001174778,0.0005454515,0.001169618,0.6340284,0.0001373907,0.001264782,0.02659701],"study_design_scores_gemma":[0.00002437001,0.0002181232,0.9292523,0.00004426178,0.0002473708,0.001373972,0.0006498458,0.003250408,0.05798347,0.00006209227,0.006880189,0.00001368617],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9917387,0.0005179374,0.001876481,0.00005901656,0.00001159866,0.00004529853,0.005001565,0.00003875845,0.0007107037],"genre_scores_gemma":[0.9867494,0.0003221374,0.005312738,0.0000968816,0.000007153633,0.00001845582,0.006775105,0.000016424,0.0007016213],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04074488,"threshold_uncertainty_score":0.08101541,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03621272714163569,"score_gpt":0.2888420375650232,"score_spread":0.2526293104233875,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}