{"id":"W3200050118","doi":"10.1099/mgen.0.000651","title":"Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":13,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Food Inspection Agency; University of Manitoba; Public Health Agency of Canada","funders":"","keywords":"Genotyping; Computational biology; SNP; Genome; Biology; SNP genotyping; Whole genome sequencing; Population; Genetics; Genotype; Single-nucleotide polymorphism; Gene; Medicine","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00008359676,0.0001647198,0.0002074935,0.00002235499,0.00009269601,0.00002659726,0.0000980596,0.0001013666,0.00001920906],"category_scores_gemma":[0.00001492001,0.0001587278,0.00006270895,0.00005498954,0.0001260606,7.994037e-7,0.0001960295,0.00005045633,0.000001773617],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000009362588,"about_ca_system_score_gemma":0.0002145639,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001140581,"about_ca_topic_score_gemma":0.00007869092,"domain_scores_codex":[0.9991528,0.00003633334,0.0002133386,0.0003388068,0.00004199726,0.0002167486],"domain_scores_gemma":[0.9994709,0.000008778222,0.00009421885,0.0002307381,0.0001389464,0.00005639797],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0001834863,0.00002988125,0.0005201023,0.00002277542,0.000134811,0.000005848941,0.0001616519,0.00003648235,0.9955584,0.00003530085,0.0001395253,0.003171769],"study_design_scores_gemma":[0.0008362384,0.0001983092,0.005242647,0.000009619353,0.00005103819,0.00009784439,0.0001172565,0.000007604053,0.9105953,0.0000235477,0.08257946,0.0002411499],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9954851,0.003404861,0.0003267671,0.00008068027,0.0001823459,0.0001050419,0.0002518496,0.000002100733,0.0001613087],"genre_scores_gemma":[0.9909211,0.002515073,0.005866133,0.000173429,0.0002710893,0.000004051491,0.0001219926,0.00002867238,0.00009850747],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.08496308,"threshold_uncertainty_score":0.6472731,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01342286083316546,"score_gpt":0.2086689526788758,"score_spread":0.1952460918457103,"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."}}