Additional file 1 of Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon

Additional file 1: Table S1. Mean discordance between imputed and actual genotypes per chromosome. Table S2. List of the 120 candidate genes tagged by the 116 significant SNPs identified with conditional and joint analysis. The P-value indicates significance of the association test performed in BOLT-LMM using a non-infinitesimal model. P-value (COJO) indicates the significance of the SNP after conditional and joint analysis. Beta and its corresponding standard error (Beta_SE) were estimated using BOLT-LMM and indicate the effect size of the minor allele. The odds ratio (OR) and its corresponding transformed standard error (SE_T) were calculated using LMOR. Table S3. List of all 512,397 SNPs in the final dataset. Output statistics from BOLT-LMM (p-value, Beta & Beta_SE) and LMOR (OR, log(OR) & SE_T) are listed. The p-value indicates significance of the association test performed in BOLT-LMM using a non-infinitesimal model. Beta and its corresponding standard error (Beta_SE) were estimated using BOLT-LMM and indicate the effect size of the minor allele. The odds ratio (OR) and its corresponding transformed standard error (SE_T) were calculated using LMOR. Table S4. Estimated heritabilities from GCTA using the 50K array dataset. Estimates are given on the observed quantitative scale and when transformed on the liability scale assuming population prevalences of 1%, 2.5% and 5%.