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).

附加文件2：表S1 本研究中中国家猪的样本信息、来源及环境变量。表S2 本研究全基因组测序数据的测序质量与读段比对统计结果。表S3 6个家猪品种不同距离区间的连锁不平衡（LD）平均水平。表S4 适应热带环境的受选择区域列表及该区域内的基因枚举。表S5 适应高海拔环境的受选择区域列表及该区域内的基因枚举。表S6 适应寒冷环境的受选择区域列表及该区域内的基因枚举。表S7 猪数量性状基因座（QTL）术语富集的热带适应特异性选择特征倍数富集值。表S8 热带适应特异性选择区域内基因的显著富集基因本体（GO）条目。表S9 猪数量性状基因座（QTL）术语富集的高海拔适应特异性选择特征倍数富集值。表S10 高海拔适应特异性选择区域内基因的显著富集基因本体（GO）条目。表S11 猪数量性状基因座（QTL）术语富集的寒冷适应特异性选择特征倍数富集值。表S12 寒冷适应特异性选择区域内基因的显著富集基因本体（GO）条目。表S13 热带适应特异性选择中ΔAF>0.7且pCADD评分较高的候选错义变异体。表S14 染色质状态富集的热带适应特异性选择特征倍数富集值。表S15 染色质状态富集的高海拔适应特异性选择特征倍数富集值。表S16 染色质状态富集的寒冷适应特异性选择特征倍数富集值。表S17 组织特异性启动子富集的热带适应特异性选择特征倍数富集值。表S18 组织特异性启动子富集的高海拔适应特异性选择特征倍数富集值。表S19 组织特异性启动子富集的寒冷适应特异性选择特征倍数富集值。表S20 不同家猪品种各组织中的ABCA1基因表达水平（数据下载自http://pig123456789.pigome.com/）。表S21 单核苷酸多态性（SNP）chr1:246,175,129周围转录因子结合位点的预测结果。