{"id":"W3197329507","doi":"10.3390/v13091790","title":"Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes","year":2021,"lang":"en","type":"article","venue":"Viruses","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":22,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Most recent common ancestor; Phylogenetic tree; Genome; Biology; Ancestor; Phylogenetics; Evolutionary biology; Coronavirus disease 2019 (COVID-19); Whole genome sequencing; Genetics; Gene; Geography; Medicine; Archaeology","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0004599211,0.0001613741,0.0004296917,0.000062325,0.0001303431,0.00005343623,0.0002112802,0.00008707833,0.00002640966],"category_scores_gemma":[0.0004005876,0.0001139017,0.00006412527,0.0002517012,0.0002376173,0.0001701631,0.0001664586,0.0002686462,0.00001886375],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004128005,"about_ca_system_score_gemma":0.0002126862,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00452896,"about_ca_topic_score_gemma":0.002667517,"domain_scores_codex":[0.9982977,0.0002801426,0.0003704656,0.0003657552,0.0004270285,0.0002589002],"domain_scores_gemma":[0.998347,0.000660543,0.0001231103,0.0007075388,0.0001279638,0.0000337806],"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":[0.0002202816,0.0001525693,0.2252191,0.00006932463,0.0000836345,0.00003809891,0.0004901693,8.631802e-8,0.7556011,0.0003396591,0.0002243726,0.0175616],"study_design_scores_gemma":[0.0009994931,0.0002076501,0.1824862,0.00006547786,0.00006206621,0.000009345566,0.0006671333,0.0000457345,0.778965,0.0005089418,0.03585605,0.0001269167],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9944358,0.003946614,0.00001746451,0.0004064385,0.0001068769,0.0001843761,0.0001118652,0.00004986958,0.0007407353],"genre_scores_gemma":[0.9631543,0.00005876485,0.0004696095,0.03598222,0.0002734578,0.00001609577,0.00001426445,0.00002446402,0.000006797974],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0427329,"threshold_uncertainty_score":0.6846462,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1679203897192879,"score_gpt":0.428701924171657,"score_spread":0.2607815344523691,"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."}}