Allele-specific expression (ASE) sites and genes in procine genome

The sites were selected by these filter criteria for further analysis: 1) total mapped reads ≥ 15 for each locus/sample; 2) minimum of 3 reads mapped to reference or alternative allele; 3) proportion of mapped reference or alternative reads accounting for > 2% of the total mapped reads. A binomial test was used to estimate significant deviation from the expected 0.5 allele ratio (with the binom.test() function in R).

The ASE sites with a false discovery rate (FDR) ≤ 0.05 were considered significant. The ASE gene were identified using phASER Gene AE 1.2.0, employing --min_haplo_maf 0.01, and utilizing the Ensembl annotation Sscrofa11.1 v104 gene features bed file as well as the filtered haplotypic count file from phASER. For the raw gene-level ASE data, similar processes were used to select the ASE gene as for ASE sites: 1) the total number of allelic reads covering each gene is ≥ 15 reads; 2) the allelic reads mapped to each haplotype are ≥ 2; 3) the proportion of reads for each haplotype accounts for > 2% of the total mapped read.