{"id":"W3092004865","doi":"10.1101/2020.10.07.329961","title":"Haploid, diploid, and pooled exome capture recapitulate features of biology and paralogy in two non-model tree species","year":2020,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genetic diversity and population structure","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary; University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; Genome Alberta; Génome Québec; Alberta Innovates; Genome British Columbia; Compute Canada; Genome Canada","keywords":"Biology; Evolutionary biology; Genome; Exome; Exome sequencing; Ploidy; Genomics; Phylogenomics; Computational biology; Phylogenetics; Genetics; Gene; Clade; 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":[0.000293625,0.000233927,0.0003231893,0.0004255542,0.0003689542,0.0003265388,0.0003011123,0.000431271,0.001400732],"category_scores_gemma":[0.0006041243,0.0001844352,0.000283442,0.0003551788,0.0002285838,0.0003774007,0.0003113832,0.0003339387,0.0002618239],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002570378,"about_ca_system_score_gemma":0.0001530538,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003618534,"about_ca_topic_score_gemma":0.01370236,"domain_scores_codex":[0.9998651,0.00001635876,0.000009581421,0.00007200561,0.00001894923,0.00001809896],"domain_scores_gemma":[0.9996572,0.0001343839,0.00004977096,0.00006581275,0.0000437592,0.00004908829],"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":[0.0005369027,0.0001355548,0.1138462,0.0001766771,0.0002920498,0.0003328512,0.0005390113,0.004518459,0.8662049,0.0005472262,0.0005500264,0.01232013],"study_design_scores_gemma":[0.00003347677,0.0002846665,0.9286564,0.00002490602,0.0002143454,0.0009548747,0.0004956377,0.01304281,0.04897016,0.0007512638,0.006512242,0.00005931452],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9929003,0.0001522792,0.004291055,0.00001993483,0.000006416354,0.00001006919,0.002052618,0.00007827648,0.0004891977],"genre_scores_gemma":[0.9890859,0.0000611175,0.005569088,0.0000855815,0.000003262898,0.00003642365,0.00444229,0.0000637673,0.0006524879],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003618534,"threshold_uncertainty_score":0.007194936,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01339807150774102,"score_gpt":0.2350105824133968,"score_spread":0.2216125109056558,"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."}}