{"id":"W4386553220","doi":"10.1270/jsbbs.23018","title":"V-primer: software for the efficient design of genome-wide InDel and SNP markers from multi-sample variant call format (VCF) genotyping data","year":2023,"lang":"en","type":"article","venue":"Breeding Science","topic":"Genetic Mapping and Diversity in Plants and Animals","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; Bio-oriented Technology Research Advancement Institution","keywords":"Biology; Indel; Primer (cosmetics); Genotyping; Genetics; Genome; Genomics; Multiplex; SNP genotyping; DNA sequencing; Computational biology; SNP; Single-nucleotide polymorphism; Amplicon; Molecular Inversion Probe; Polymerase chain reaction; DNA; Genotype; Gene","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.007931257,0.003926162,0.002927304,0.004172423,0.00130581,0.002459682,0.004539332,0.002606168,0.03851575],"category_scores_gemma":[0.009473508,0.004969269,0.002718589,0.002818569,0.001176544,0.002947949,0.002740126,0.005188354,0.02956],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001124603,"about_ca_system_score_gemma":0.002749767,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001707231,"about_ca_topic_score_gemma":0.002710928,"domain_scores_codex":[0.9963776,0.001056521,0.0005691209,0.001075085,0.0006018991,0.0003198921],"domain_scores_gemma":[0.9962131,0.002375673,0.0005177117,0.0003285238,0.0004281237,0.0001370037],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.004547561,0.0006875078,0.007499877,0.0123944,0.00203174,0.001917346,0.002108829,0.01254738,0.2125944,0.03071397,0.3755212,0.3374358],"study_design_scores_gemma":[0.001139778,0.0005641585,0.006291621,0.001418143,0.0006243541,0.002866428,0.0002710709,0.06099276,0.1683601,0.03717382,0.7195314,0.0007663611],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.004374921,0.00205286,0.7888893,0.0002906009,0.0003966324,0.001085421,0.03711126,0.1612173,0.004581637],"genre_scores_gemma":[0.01094835,0.0007758027,0.911641,0.0005429639,0.000068282,0.00327162,0.0416669,0.02667653,0.00440854],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.03851575,"threshold_uncertainty_score":0.128848,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1048904541315576,"score_gpt":0.2881530785682789,"score_spread":0.1832626244367213,"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."}}