Gene Annotation and Enrichment Analysis

Gene-based and region-based annotations were conducted for all detected SVs in ANNOVAR v 2019Oct24 (Wang et al., 2010). There were 63,041 transcripts (including 13,184 transcripts without coding sequence annotations) for 31,907 unique genes within the Duroc genome used to annotate SVs, and the genes were downloaded from the Ensemble database (S. scrofa 11.1). We performed gene enrichment analysis for the annotated genes with KOBAS v3.0 (Mao et al., 2005). We used Fisher's exact test and hypergeometric test as the significance test method. The Benjamini-Hochberg and Benjamini-Yekutieli methods were applied to correct the false discovery rate. Pathways with corrected P-values smaller than 0.05 were considered to be significant.