Additional file 3 of Mapping and functional characterization of structural variation in 1060 pig genomes

Additional file 3: Table S13. Locations of SV-related enhancers and promoters. Table S14. Proportions of SV-related regulators in various locations of tissues. Table S15. Statistics of SV-related QTL. Table S16. QTL mapping SV for individual genome. Table S17. Locations of group-specific or high FST SVs. Table S18. Summary of group-specific or group-differential SVs. Table S19. GO enrichment results of genes in group-specific or group-differential SVs. Table S20. KEGG pathway analysis of genes mapping/flanking group-specific or group-differential SVs. Table S21. RNA-seq sample list in AS and EU ancestral group comparison. Table S22. Statistics of RNA-seq samples for AS and EU comparison. Table S23. The SV and gene list for AS and EU comparison. Table S24. SV-related DEGs for AS and EU ancestral group comparison. Table S25. Statistics of multiple-tissue SV-related DEGs between AS and EU groups. Table S26. Statistics of SV-related multiple-tissue DEGs with discordant expression levels between tissues. Table S27. TWAS annotation of SV-related multiple-tissue DEGs between AS and EU pigs. Table S28. Allele frequency of MYO5A DEL in each population. Table S29. RNA-seq sample list in SV-related analyses for sub-populations. Table S30. SV-related DEGs for sub-population comparisons. Table S31. Length statistics for chromatin states in the chr8:130924619-130980283 DUP region. Table S32. Median r2 values for 1060 pigs, 425 EUC pigs, and 187 Yorkshire pigs at different genomic distances. Table S33. Proportions of SV with linked, tagged, and highly-tagged r2 with SNPs. Table S34. Proportions of SV with linked, tagged, and highly-tagged r2 with functional SNPs. Table S35. List of SV-linked functional SNPs with multiple signals for 1060 pigs. Table S36. List of SV directly overlapped e/sGenes for their linked SNPs in 1060 pigs. Table S37. List of the 51 bp DEL overlapped enhancers in 14 tissues. Table S38. List of the 51 bp DEL-linked SNPs. Table S39. List of QTLs mapped within the 2 Mb region. Table S40. List of SV-linked functional SNPs with multiple signals for 425 EUC pigs. Table S41. List of SV-linked functional SNPs with multiple signals for 187 Yorkshire pigs. Table S42. MYO5A functions based on GWAS results of EMBL-EBI. Table S43. List of data information for all analyzed samples. Table S44. Pig genome bad bins in our dataset. Table S45. All analyzed genes.