Additional file 2 of Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs

Additional file 2: Table S1. Samples, origin, and environmental variables of Chinese pigs in this study. Table S2. The sequencing quality and read alignment statistic of whole-genome sequencing data in this study. Table S3. The average value of LD in different distance regions among 6 domestic pig breeds. Table S4. List of regions under selection for adaptation to tropical environments and enumeration of the genes within such regions. Table S5. List of regions under selection for adaptation to high-altitude environments and enumeration of the genes within such regions. Table S6. List of regions under selection for adaptation to frigid environments and enumeration of the genes within such regions. Table S7. Fold enrichment of tropical adaptation-specific selection signatures for pig QTL terms. Table S8. Significantly enriched GO terms of the genes in tropical adaptation-specific selection regions. Table S9. Fold enrichment of high-altitude adaptation-specific selection signatures for pig QTL terms. Table S10. Significantly enriched GO terms of the genes in high-altitude adaptation-specific selection regions. Table S11. Fold enrichment of frigid adaptation-specific selection signatures for pig QTL terms. Table S12. Significantly enriched GO terms of the genes in frigid adaptation-specific selection regions. Table S13. Candidate nonsynonymous variants (ΔAF > 0.7) of tropical adaptation-specific selection with high pCADD score. Table S14. Fold enrichment of tropical adaptation-specific selection signatures for chromatin states. Table S15. Fold enrichment of high-altitude adaptation-specific selection signatures for chromatin states. Table S16. Fold enrichment of frigid adaptation-specific selection signatures for chromatin states. Table S17. Fold enrichment of tropical adaptation-specific selection signatures for tissue-specific promoters. Table S18. Fold enrichment of high-altitude adaptation-specific selection signatures for tissue-specific promoters. Table S19. Fold enrichment of frigid adaptation-specific selection signatures for tissue-specific promoters. Table S20. ABCA1 expression levels across various tissues in different pig breeds (Download from http://pig123456789.pigome.com/ ). Table S21. Prediction of the transcription factors binding around the SNP (chr1:246,175,129).