{"id":"W3136786679","doi":"10.1186/s13040-021-00251-0","title":"Indels in SARS-CoV-2 occur at template-switching hotspots","year":2021,"lang":"en","type":"article","venue":"BioData Mining","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":39,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University","funders":"National Science Foundation of Sri Lanka; Stanford Bio-X; National Science Foundation","keywords":"Indel; Genetics; Biology; RNA; Computational biology; Homologous recombination; RNA polymerase; Recombination; Evolutionary biology; Gene; Single-nucleotide polymorphism; Genotype","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005881471,0.0002336666,0.0004281366,0.000335921,0.0001299057,0.00008756403,0.0002798181,0.0002032894,0.00003733936],"category_scores_gemma":[0.0006607117,0.0002251014,0.00009417207,0.0008038072,0.0000542124,0.000254126,0.0005544227,0.0004251776,0.0003258644],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002396129,"about_ca_system_score_gemma":0.0004819572,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003396104,"about_ca_topic_score_gemma":0.000555017,"domain_scores_codex":[0.997633,0.0000885444,0.0004368836,0.0006724215,0.0005310462,0.0006381528],"domain_scores_gemma":[0.9987676,0.0002147418,0.00008056161,0.0007849624,0.0001011139,0.00005108747],"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":[0.0001995583,0.0001104359,0.2749416,0.0001134398,0.0000476434,0.002157266,0.0008988772,1.542323e-7,0.7078355,0.00002290926,0.003057898,0.01061468],"study_design_scores_gemma":[0.00286296,0.0001212814,0.04115409,0.000560822,0.00004013232,0.0004042046,0.0009585819,0.0007303421,0.785057,0.0000347399,0.1676893,0.0003865857],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9934157,0.0009689867,0.00009761504,0.0004627011,0.0002078519,0.0002106216,0.00003657556,0.00008058277,0.004519425],"genre_scores_gemma":[0.9728529,0.00001224397,0.001274195,0.02545524,0.0001946823,0.00002309971,0.00005234976,0.00004273136,0.00009254414],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2337875,"threshold_uncertainty_score":0.9179369,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.121934235703093,"score_gpt":0.3875826429091648,"score_spread":0.2656484072060718,"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."}}