{"id":"W2409454759","doi":"10.1016/j.meegid.2016.06.015","title":"Deep sequencing increases hepatitis C virus phylogenetic cluster detection compared to Sanger sequencing","year":2016,"lang":"en","type":"article","venue":"Infection Genetics and Evolution","topic":"Hepatitis C virus research","field":"Medicine","cited_by":15,"is_retracted":false,"has_abstract":false,"ca_institutions":"St. Paul's Hospital; BC Centre for Disease Control; University of British Columbia","funders":"Canadian Institutes of Health Research","keywords":"Viral quasispecies; Deep sequencing; Sanger sequencing; Biology; Phylogenetic tree; Population; Metagenomics; DNA sequencing; Genetics; Single cell sequencing; Evolutionary biology; Computational biology; Hepatitis C virus; Genome; Virus; Exome sequencing; Gene; Medicine; Mutation","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":[0.0002767748,0.0001821808,0.0002252162,0.0003690117,0.0002223751,0.00004490318,0.00003986285,0.0001450206,0.0001101715],"category_scores_gemma":[0.000275956,0.0001516042,0.00006257972,0.0003423963,0.00008381026,0.0001053977,0.00007513409,0.0001219999,0.0001630961],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001421447,"about_ca_system_score_gemma":0.0001456893,"about_ca_topic_candidate":true,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01170947,"about_ca_topic_score_gemma":0.0162885,"domain_scores_codex":[0.9984262,0.0001444409,0.0003201253,0.0003851329,0.0003497611,0.0003743649],"domain_scores_gemma":[0.9989807,0.00007759276,0.00007161927,0.0002591783,0.0003005642,0.0003103437],"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":[0.00007445281,0.00002488161,0.4382077,0.00004063361,0.00003207927,0.000006008092,0.00009929663,0.0004237527,0.4976583,0.000008441353,0.00008425493,0.06334025],"study_design_scores_gemma":[0.001229609,0.0006709656,0.8912277,0.0002075499,0.0000803724,0.0001401375,0.00002137965,0.02897696,0.07417873,0.000237731,0.002735817,0.0002930041],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8788921,0.0003322683,0.1194282,0.0001308786,0.0001972112,0.0005096768,0.00001100996,0.00009158809,0.0004071257],"genre_scores_gemma":[0.9969546,0.001263335,0.0009833936,0.0002253149,0.000330834,0.00008383445,0.000007266622,0.00003434757,0.0001170724],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4530201,"threshold_uncertainty_score":0.9948716,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03103999025387206,"score_gpt":0.2886373789180233,"score_spread":0.2575973886641512,"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."}}