{"id":"W2296792180","doi":"10.1101/027318","title":"Utilization of high throughput genome sequencing technology for large scale single nucleotide polymorphism discovery in red deer and Canadian elk","year":2015,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genetic and phenotypic traits in livestock","field":"Biochemistry, Genetics and Molecular Biology","cited_by":36,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"AgResearch","keywords":"Genotyping; Genome; Bovine genome; SNP genotyping; Biology; Single-nucleotide polymorphism; Reference genome; Genetics; DNA sequencing; Molecular Inversion Probe; Whole genome sequencing; Tag SNP; Sequence assembly; SNP; Computational biology; Gene; Genotype; Transcriptome","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003115243,0.000322051,0.0003962041,0.0002684631,0.00007217625,0.00004314706,0.0003197145,0.000723708,0.000003940317],"category_scores_gemma":[0.0001303645,0.0003699132,0.00005960884,0.000222814,0.0001352702,0.00001207786,0.0002924908,0.0002152449,9.636317e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001983059,"about_ca_system_score_gemma":0.001091284,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001558518,"about_ca_topic_score_gemma":0.00290438,"domain_scores_codex":[0.9982021,0.00005147774,0.0004039403,0.0007390684,0.0001196701,0.0004837163],"domain_scores_gemma":[0.9985924,0.00001041485,0.0002328015,0.0007017578,0.0002868215,0.0001758381],"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":[0.00005154768,0.00008055534,0.01089297,0.0002114123,0.00008022774,0.000002750751,0.00003373237,0.0003785019,0.9858555,0.002308624,0.0000985243,0.000005701446],"study_design_scores_gemma":[0.002074983,0.0005163793,0.2247508,0.0003534433,0.0001578587,1.723804e-7,0.00006990021,0.0001521058,0.7624952,0.0005378844,0.007658549,0.001232671],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9857089,0.002842991,0.009367748,0.0001685954,0.0004245862,0.0006865262,0.0007587728,0.00002743881,0.00001446431],"genre_scores_gemma":[0.9760735,0.000101889,0.02332995,0.0000883746,0.0002218161,0.0000867239,0.000009135229,0.00007707289,0.00001151283],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2233602,"threshold_uncertainty_score":0.9998753,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01743176717344663,"score_gpt":0.2178533069937421,"score_spread":0.2004215398202954,"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."}}