Additional file 1 of Evaluation of heritability partitioning approaches in livestock populations

Additional file 1. Supplementary Tables. Table S1. %SNP heritability estimation when variants in open chromatin regions account for 50% of the heritability. Table S2. %SNP heritability estimation when causal variants are enriched in low MAF variants. Table S3. %SNP heritability estimation when causal variants are enriched in low LD score variants. Table S4. %SNP heritability estimation when causal variants are enriched in low MAF and LD score variants. Table S5. %SNP heritability estimation when causal variants are enriched in common variants. Table S6. %SNP heritability estimation when causal variants are enriched in high LD score variants. Table S7. %SNP heritability estimation when causal variants are enriched in low MAF and high LD score variants. Table S8. %SNP heritability estimation with multiple functional categories when the variants in coding sequence account for 100% of the heritability. Table S9. %SNP heritability estimation with multiple functional categories when the variants in intronic regions account for 100% of the heritability. Table S10. %SNP heritability estimation with multiple functional categories when the variants in upstream and downstream regions account for 100% of the heritability. Table S11. %SNP heritability estimation with multiple functional categories when the variants in intergenic regions account for 100% of the heritability. Table S12. %SNP heritability estimation with multiple functional categories when the variants in open chromatin regions account for 100% of the heritability. Table S13. %SNP heritability estimation with multiple functional categories when the variants from different functional classes had equal contribution. Table S14. %SNP heritability estimation in complex simulation scenarios where SNPs from different functional classes had variable contributions (scenario I). Table S15. %SNP heritability estimation in complex simulation scenarios where SNPs from different functional classes had variable contributions (scenario II). Table S16. %SNP heritability estimation in complex simulation scenarios where SNPs from different functional classes had variable contributions (scenario III). Table S17. Mean Absolute Error of %SNP heritability estimates across the three complex simulation scenarios where SNPs from different functional classes had variable contributions. Table S18. %SNP heritability estimation with a two-component approach when the variants from different functional classes had equal contribution. Table S19. %SNP heritability estimation with a two-component approach in complex simulation scenarios where SNPs from different functional classes had variable contributions (scenario I). Table S20. %SNP heritability estimation with a two-component approach in complex simulation scenarios where SNPs from different functional classes had variable contributions (scenario II). Table S21. %SNP heritability estimation with a two-component approach in complex simulation scenarios where SNPs from different functional classes had variable contributions (scenario III). Table S22. Mean Absolute Error of %SNP heritability estimates using a two-component approach across the three complex simulation scenarios where SNPs from different functional classes had variable contributions. Table S23. Correlations between genomic relationship matrices from different functional categories. Table S24. %SNP heritability estimation for the measured phenotypes. Table S25. Heritability enrichment estimation for the measured phenotypes. Table S26. %SNP heritability and heritability enrichment estimation using a LDMS two component approach for the measured phenotypes.

附加文件1：补充表格。
表S1：开放染色质区域（open chromatin regions）内的变异占遗传力50%时的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）遗传力百分比估算。
表S2：当因果变异富集于低次要等位基因频率（Minor Allele Frequency, MAF）变异时的SNP遗传力百分比估算。
表S3：当因果变异富集于低连锁不平衡得分（Linkage Disequilibrium Score, LD score）变异时的SNP遗传力百分比估算。
表S4：当因果变异同时富集于低次要等位基因频率与低连锁不平衡得分变异时的SNP遗传力百分比估算。
表S5：当因果变异富集于常见变异时的SNP遗传力百分比估算。
表S6：当因果变异富集于高连锁不平衡得分变异时的SNP遗传力百分比估算。
表S7：当因果变异同时富集于低次要等位基因频率与高连锁不平衡得分变异时的SNP遗传力百分比估算。
表S8：当编码序列（coding sequence）内的变异占全部遗传力时，基于多功能类别的SNP遗传力百分比估算。
表S9：当内含子区域（intronic regions）内的变异占全部遗传力时，基于多功能类别的SNP遗传力百分比估算。
表S10：当上下游区域内的变异占全部遗传力时，基于多功能类别的SNP遗传力百分比估算。
表S11：当基因间区域（intergenic regions）内的变异占全部遗传力时，基于多功能类别的SNP遗传力百分比估算。
表S12：当开放染色质区域内的变异占全部遗传力时，基于多功能类别的SNP遗传力百分比估算。
表S13：当来自不同功能类别的变异贡献均等时，基于多功能类别的SNP遗传力百分比估算。
表S14：来自不同功能类别的单核苷酸多态性具有可变贡献的复杂模拟场景（场景I）中的SNP遗传力百分比估算。
表S15：来自不同功能类别的单核苷酸多态性具有可变贡献的复杂模拟场景（场景II）中的SNP遗传力百分比估算。
表S16：来自不同功能类别的单核苷酸多态性具有可变贡献的复杂模拟场景（场景III）中的SNP遗传力百分比估算。
表S17：在来自不同功能类别的单核苷酸多态性具有可变贡献的三类复杂模拟场景中，SNP遗传力百分比估算的平均绝对误差。
表S18：当来自不同功能类别的变异贡献均等时，采用双组分方法的SNP遗传力百分比估算。
表S19：在来自不同功能类别的单核苷酸多态性具有可变贡献的复杂模拟场景（场景I）中，采用双组分方法的SNP遗传力百分比估算。
表S20：在来自不同功能类别的单核苷酸多态性具有可变贡献的复杂模拟场景（场景II）中，采用双组分方法的SNP遗传力百分比估算。
表S21：在来自不同功能类别的单核苷酸多态性具有可变贡献的复杂模拟场景（场景III）中，采用双组分方法的SNP遗传力百分比估算。
表S22：在来自不同功能类别的单核苷酸多态性具有可变贡献的三类复杂模拟场景中，采用双组分方法得到的SNP遗传力百分比估算的平均绝对误差。
表S23：不同功能类别对应的基因组关系矩阵（genomic relationship matrices）之间的相关性。
表S24：实测表型（measured phenotypes）的SNP遗传力百分比估算。
表S25：实测表型的遗传力富集估算。
表S26：采用LDMS双组分方法对实测表型进行SNP遗传力百分比与遗传力富集估算。