{"id":"W7108314877","doi":"10.6084/m9.figshare.30759582","title":"Additional file 1 of Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi","year":2025,"lang":"","type":"article","venue":"Open MIND","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"","keywords":"Table (database); Whole genome sequencing; Genotyping; Genome; Salmonella typhi; Typhoid fever; Typing; Identification (biology)","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.001654304,0.001250665,0.001121889,0.002151761,0.001077056,0.001561989,0.002137987,0.001107996,0.797159],"category_scores_gemma":[0.01501485,0.000694842,0.0009113759,0.003368306,0.0002881937,0.00175116,0.001446914,0.001068674,0.2008751],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008450699,"about_ca_system_score_gemma":0.001646391,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006745156,"about_ca_topic_score_gemma":0.01336504,"domain_scores_codex":[0.999279,0.00009424886,0.0001020809,0.0002290625,0.0001766095,0.0001189796],"domain_scores_gemma":[0.9919252,0.004877727,0.0006350963,0.0008738564,0.001327139,0.0003610603],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0003998649,0.00008715311,0.002969406,0.003040218,0.00005310974,0.00009340564,0.00009813906,0.0004836936,0.001197804,0.0005423226,0.9803413,0.01069354],"study_design_scores_gemma":[0.002023077,0.0003161312,0.0391784,0.002599726,0.0001857837,0.0006587,0.0004882201,0.002761703,0.005568446,0.00552882,0.9404922,0.0001987861],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"dataset","genre_gemma":"dataset","genre_scores_codex":[0.0002953458,0.00001687362,0.0006536609,0.00006001098,0.00002975676,0.0000652274,0.9971323,0.000941154,0.0008057234],"genre_scores_gemma":[0.004836066,0.00006960787,0.005772157,0.0003316024,0.00006648278,0.0006467493,0.9809921,0.002342918,0.00494227],"genre_candidate":"dataset","genre_consensus":"dataset","teacher_disagreement_score":0.797159,"threshold_uncertainty_score":0.2893281,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05592655117993615,"score_gpt":0.2974729157765596,"score_spread":0.2415463645966235,"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."}}