X-LDR: an atlas of linkage disequilibrium across species

To reach a genomic scale illustration for linkage disequilibrium (LD), we introduce X-LDR, a stochastic algorithm for biobank-scale data ([Formula: see text], n the sample size, m the number of SNPs, and B iterations). X-LDR can scale the entire genome to high-resolution LD grids, such as nearly 9 million LD grids for UK Biobank ([Formula: see text] and [Formula: see text] million). Various characteristics of LD are discovered in terms of their biological annotation. We also present an unprecedented LD atlas for 25 reference populations that contours the diversity of interspecies LD. The algorithms have been implemented in C++.