Allele frequency differentiation among ancestry components in 1000 Genomes Project

This repository contains results from applying the selscan tool from Ohana (Cheng et al., 2022) to genotype data from 2,504 unrelated individuals from the 1000 Genomes Project Phase 3 dataset. The matrix of ancestral component proportions per sample was inferred from pruned variants (n = 106,740) on chr21 and is provided in chr21_pruned_50_Q.matrix (see Methods of Yan et al., 2021) and the inferred matrix of allele frequencies for these variants is provided in chr21_pruned_50_F.matrix. The Q matrix is visualized in Figure 3A of Yan et al. (2021). The file samples.txt contains sample identifiers in the order necessary to interpret these previous files. Files named chr*_ohana_scan.tsv.gz contain the results of the selscan tool, where the focal ancestral component is recorded in the last column. The column "lle_ratio" records log likelihood ratios, quantifying the extent to which allele frequencies of individual variants are better explained by the genome-wide covariance matrix or by an alternative covariance matrix where allele frequencies are allowed to vary in one of each of eight ancestry components. Higher values reflect support for the latter model. References Cheng, J. Y., Stern, A. J., Racimo, F., & Nielsen, R. (2022). Detecting selection in multiple populations by modeling ancestral admixture components. Molecular biology and evolution, 39(1), msab294. Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C., & McCoy, R. C. (2021). Local adaptation and archaic introgression shape global diversity at human structural variant loci. Elife, 10, e67615.本仓库收录了将Ohana开发的selscan工具（Cheng等，2022）应用于千人基因组计划第三阶段数据集的2504名无关个体基因型数据所得的分析结果。 每个样本的祖先组分占比矩阵基于21号染色体上经过连锁不平衡修剪的变异位点（共106740个）推断得到，存储于文件chr21_pruned_50_Q.matrix（详见Yan等2021年的研究方法）；上述变异位点的等位基因频率推断矩阵则存储于chr21_pruned_50_F.matrix。该Q矩阵已在Yan等（2021）的图3A中完成可视化展示。文件samples.txt按照解读前述文件所需的顺序存储了样本标识符。 命名为chr*_ohana_scan.tsv.gz的文件包含selscan工具的运行结果，其中最后一列记录了焦点祖先组分。列"lle_ratio"记录对数似然比，用于量化单个变异位点的等位基因频率更适合用全基因组协方差矩阵解释，还是用另一种协方差矩阵（允许8个祖先组分中任意一个的等位基因频率发生变异）解释。比值越高，越支持后一种模型。 参考文献 Cheng, J. Y., Stern, A. J., Racimo, F., & Nielsen, R. (2022). 通过建模祖先混血组分检测多群体选择信号. 分子生物学与进化, 39(1), msab294. Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C., & McCoy, R. C. (2021). 局部适应与古基因渗入塑造人类结构变异位点的全球多样性. eLife, 10, e67615.