{"id":"W4365135538","doi":"10.1099/mgen.0.000979","title":"Comparing genomic variant identification protocols for Candida auris","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antifungal resistance and susceptibility","field":"Medicine","cited_by":15,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Commissariat Général à l'Investissement; Centers for Disease Control and Prevention; Agence Nationale de la Recherche; National Institute of Allergy and Infectious Diseases; Division of Intramural Research, National Institute of Allergy and Infectious Diseases; Broad Institute; Wellcome Trust; Medical Research Council; Canadian Institute for Advanced Research; National Institutes of Health; U.S. Department of Health and Human Services","keywords":"Biology; Single-nucleotide polymorphism; Phylogenetic tree; Clade; Computational biology; Genetics; Concordance; Genome-wide association study; SNP; Population; Gene; Medicine; Genotype","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00049362,0.0001373107,0.0003080823,0.00009630928,0.000180909,0.00005976743,0.0001727444,0.00009455623,0.00003252103],"category_scores_gemma":[0.0001048082,0.0001388425,0.0001440945,0.0001887835,0.00005664048,0.00004645262,0.00008447807,0.0001119494,0.000297387],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003054801,"about_ca_system_score_gemma":0.0002475507,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00007209184,"about_ca_topic_score_gemma":0.0001695887,"domain_scores_codex":[0.99878,0.00002125566,0.0004048429,0.0003674714,0.00008624679,0.0003402298],"domain_scores_gemma":[0.9991886,0.00003992396,0.0001079315,0.0004660244,0.0001031176,0.00009440644],"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":[0.0005613426,0.00006686659,0.01347505,0.0002694634,0.00004548788,0.00001197193,0.0003567604,0.00004803048,0.9704276,0.0001436212,0.01344655,0.001147234],"study_design_scores_gemma":[0.006373672,0.000374681,0.5988068,0.0002288113,0.0002661738,0.00006923959,0.0005287351,0.007947581,0.1619975,0.001082817,0.2215699,0.0007541188],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.984131,0.00002190753,0.003772186,0.0004135262,0.0001861681,0.01096419,0.00008675944,0.000135084,0.0002891989],"genre_scores_gemma":[0.9923751,0.00001827307,0.001595072,0.000169951,0.0003357525,0.001559821,0.0002962339,0.00004217964,0.003607621],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8084301,"threshold_uncertainty_score":0.5661831,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0570976395604316,"score_gpt":0.3247589607406333,"score_spread":0.2676613211802017,"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."}}