{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002884707,0.0007033317,0.001000852,0.001014532,0.000560909,0.001706999,0.0004752401,0.001169915,0.005381328],"category_scores_gemma":[0.006342485,0.001062932,0.0008389013,0.0005262578,0.0005818593,0.001493584,0.001693557,0.001681441,0.001900404],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000546352,"about_ca_system_score_gemma":0.0006562221,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001435429,"about_ca_topic_score_gemma":0.005537838,"domain_scores_codex":[0.9975336,0.0008926167,0.0001057567,0.0005651196,0.0006966339,0.0002063984],"domain_scores_gemma":[0.9954216,0.002975056,0.0002132074,0.0006304521,0.0005281999,0.0002315093],"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":[0.001138087,0.0003445812,0.0346415,0.000458656,0.0004233012,0.00008634063,0.000304604,0.003376883,0.819473,0.001882991,0.005081175,0.1327888],"study_design_scores_gemma":[0.0002905307,0.001090429,0.1352575,0.0002784282,0.0009512281,0.001596982,0.0004321639,0.1718071,0.6161518,0.01239529,0.05954093,0.0002076012],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6321253,0.004811209,0.3254522,0.002581756,0.0009153506,0.0003466359,0.006999751,0.006068754,0.02069909],"genre_scores_gemma":[0.6632808,0.001188801,0.3155898,0.003408108,0.0002645626,0.0002338616,0.005267847,0.001059476,0.009706895],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005381328,"threshold_uncertainty_score":0.01800227,"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."}}