Fig. 3

Manhattan plots and Quantile-Quantile (QQ) plots for six phenotypes of pig biological characteristics. There were three types of genome variants plotted in Manhattan plots, in which blue triangles represent CNVs, green diamonds represent InDels, and purple circles represent SNPs. Only the genome variants with genome-wide significant P-values were plotted in Manhattan plots, and the P-values were corrected by the Bonferroni cutoff, which was defined by 0.05/N, where N represents the number of genome variants for each independent GWAS. For QQ plots, the X-axis represents the expected −log₁₀(P), and the y-axis represents the observed −log₁₀(P)