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

It contains all ASE sites and genes across 6020 pig individuals spanning 42 tissues (including 3 cell lines) and 34 breeds from the Farm-GTEx-pig project.SNP-level ASE was generated using the phASER (version 1.1.1) package. 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. The remaining genes (termed ‘tested gene’) were tested for significant imbalanced expression using binomial tests, and p values were corrected using the Benjamini-Hochberg method, and ASE genes with FDR ≤ 0.05 were considered significantly imbalanced.The "6020.ASE.site.sum.sort.pCADD.txt.gz" contains "chr position refAllele altAllele refCount altCount totalCount ref_ratio p-value FDR SampleID Breed Tissue pCADD'"The "6020.ASE.gene.sum.sort.txt.gz" contains “chr start stop GeneID aCount bCount totalCount log2_aFC p-valueFDR SampleID Breed Tissue”