{"id":"W2734886065","doi":"10.1093/bioinformatics/btx254","title":"Discovery and genotyping of novel sequence insertions in many sequenced individuals","year":2017,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":36,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; Simon Fraser University","funders":"Türkiye Bilimsel ve Teknolojik Araştırma Kurumu; European Molecular Biology Organization","keywords":"Structural variation; Sequence assembly; Sequence (biology); Reference genome; Genome; Computational biology; Breakpoint; Computer science; Genotyping; Biology; Zygosity; Hybrid genome assembly; DNA sequencing; Genetics; Whole genome sequencing; Algorithm; Genotype; 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001276361,0.00008581614,0.0001176073,0.00003438522,0.000120609,0.0000501439,0.0001860937,0.00006414827,4.367117e-7],"category_scores_gemma":[0.00009597315,0.00007933751,0.00002666276,0.00002091148,0.0001554727,0.00000675976,0.0002374899,0.00003760681,6.423233e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000006480092,"about_ca_system_score_gemma":0.00004812884,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005295149,"about_ca_topic_score_gemma":0.00005052777,"domain_scores_codex":[0.9994797,0.000004867112,0.0002364436,0.00009025644,0.00005939474,0.000129332],"domain_scores_gemma":[0.9994436,0.000007428868,0.0001757988,0.0003166756,0.000031785,0.00002471292],"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":[0.00001555304,0.00004460782,0.1086353,0.0001081356,0.00005748437,5.645734e-7,0.0008788849,0.0001296891,0.8859472,0.001622619,0.00003978125,0.002520197],"study_design_scores_gemma":[0.001525929,0.0002152366,0.8379688,0.0001188144,0.00003055601,0.00002260127,0.0007719456,0.002889583,0.1537555,0.0004831751,0.001789015,0.0004289042],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9970621,0.0002767333,0.001429382,0.00007430703,0.00005555532,0.0001137119,0.00008238039,0.000001056655,0.0009047015],"genre_scores_gemma":[0.9886057,0.0004016347,0.01082918,0.00007306368,0.00002195472,0.000006727916,0.00001231796,0.000005175012,0.00004420421],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7321917,"threshold_uncertainty_score":0.3235289,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04019711173590731,"score_gpt":0.2830124640901386,"score_spread":0.2428153523542313,"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."}}