Additional file 3: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Table S1. RNA-seq reads mapped to different bovine genome origins. (XLSX 14 kb

Additional file 7: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Table S5. Genes that display significant differential splicing between breeds. (XLSX 38 kb

Additional file 10: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Table S8. SNP overlap between expression QTLs and SNPs with pleiotropic effects on conventional traits of dairy cattle. (XLSX 38 kb

Additional file 4: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Table S2. Splicing junction annotation analysis using BAM files generated by different alignment software. (XLSX 13 kb

Additional file 8: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Table S6. Summary of significant cis splicing sQTLs (within 1 Mb distance to the exon). (XLSX 14902 kb

Additional file 6: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Table S4. Genes that display significant differential splicing cross tissues. (XLSX 18699 kb

Additional file 1: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Supplementary Methods. (DOCX 42 kb

Additional file 9: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Table S7. Summary table for count values of sQTLs and eeQTLs in white blood and milk cells. (XLSX 9 kb

Additional file 5: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Table S3. 2 × 2 tables for the overlap between exon and intron analyses. (XLSX 15 kb

Additional file 2: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Figure S1. Gene coverage uniformity plots for each tissue type for a) all genes, b) 500 highest expressed genes and c) 500 lowest expressed genes, as determined by Qualimap 2 [1]. Figure S2. Splicing junction saturation analysis for each tissue type for a) all splicing junctions, b) known splicing junctions and c) novel splicing junctions. Figure S3. The distribution of concordance between imputed and RNA sequence genotypes. Figure S4. Sample principal components clustering based on exon expression. Figure S5. Correlation of sQTLs (splicing quantitative trait loci), eeQTLs (exon expression QTLs) and geQTLs (gene expression QTLs) effects (t values) between tissues. Figure S6. Sharing of sQTLs (splicing quantitative trait loci), eeQTLs (exon expression QTLs) and geQTLs (gene expression QTLs) in paired tissues at p < 0.05 level. Figure S7. Manhattan plot of eeQTLs for the MGST1 gene. (PDF 737 kb