{"id":"W2115610250","doi":"10.1038/nmeth.1185","title":"SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries","year":2008,"lang":"en","type":"article","venue":"Nature Methods","topic":"Genetic and phenotypic traits in livestock","field":"Biochemistry, Genetics and Molecular Biology","cited_by":676,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Alberta","funders":"","keywords":"Genetics; Biology; Single-nucleotide polymorphism; Genotyping; SNP genotyping; Allele frequency; Genome; Genotype; DNA sequencing; SNP; Deep sequencing; Allele; Population; Computational biology; Gene","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002840537,0.000773442,0.001317009,0.001579935,0.0007010394,0.001544741,0.001299045,0.001212077,0.001542565],"category_scores_gemma":[0.006731735,0.0008201891,0.001290881,0.001331621,0.000730234,0.0007729993,0.001705982,0.00236743,0.0008097208],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005342435,"about_ca_system_score_gemma":0.0009724883,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001215371,"about_ca_topic_score_gemma":0.003316447,"domain_scores_codex":[0.9977241,0.0008508894,0.00009938929,0.0006576892,0.0004689106,0.0001990473],"domain_scores_gemma":[0.9966357,0.00183321,0.0003278765,0.0007557945,0.0002642833,0.0001831919],"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":[0.001538598,0.0004918271,0.03411826,0.0004457778,0.0008579776,0.0003852241,0.0006442438,0.03237966,0.5650182,0.02731923,0.003524558,0.3332765],"study_design_scores_gemma":[0.0002713175,0.0005787461,0.05933121,0.00008069231,0.0005762331,0.001024385,0.0001817732,0.5916518,0.2379953,0.09128094,0.01677393,0.0002536769],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.1878235,0.0003393455,0.8057066,0.0002896228,0.00006813141,0.00009847236,0.002016965,0.001909433,0.001747948],"genre_scores_gemma":[0.524267,0.0002436023,0.466563,0.0004482742,0.00005722401,0.0003075542,0.004591385,0.0004291154,0.003092804],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.002840537,"threshold_uncertainty_score":0.01502234,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02242832749851655,"score_gpt":0.3323102235550311,"score_spread":0.3098818960565146,"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."}}