Additional file 4 of Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle

Additional file 4: Table S10. Minor allele frequencies and allele effects for WGS tag variants with a significant association effect in FT-MIR wavenumbers and a co-localized eQTL. Table S11. Association statistic profiles for 38 loci with a co-localized eQTL for at least one FT-MIR wavenumber phenotype. The proportion of phenotypic and genetic variance accounted for by each locus is shown for each of the 895 FT-MIR wavenumber and three FT-MIR predicted milk composition phenotypes. The genetic variance for each phenotype is the SNP-based estimate evaluated by the Bolt-LMM software. Table S12. Chronological profiles across iterations for 19 significant association effects with a co-localized eQTL observed in FT-MIR wavenumbers, where the association is observed after fitting the top chromosomal variant(s) in previous GWAS iterations and/or the base GWAS as covariates. Iterations are defined relative to the base GWAS, with the base GWAS represented as iteration 0. P-values at previous iterations for the phenotype, and p-values for the corresponding top chromosomal SNP in that iteration are provided. Table S13. Minor allele frequencies and allele effects for WGS tag variants with a significant association effect in at least one FT-MIR predicted milk composition trait and a co-localized eQTL. FP = Fat %; LP = Lactose %; PP = Protein %. Table S14. Chronological profiles across iterations for 12 significant association effects with a co-localized eQTL observed in FT-MIR predicted milk composition traits, where the association is observed after fitting the top chromosomal variant(s) in previous GWAS iterations and/or the base GWAS as covariates. Iterations are defined relative to the base GWAS, with the base GWAS represented as iteration 0. P-values at previous iterations for the phenotype, and p-values for the corresponding top chromosomal SNP in that iteration have been provided. FP = Fat %; LP = Lactose %; PP = Protein %.