Figure 2.

LD pattern among low frequency alleles and common alleles. The proportions of pair-wise SNPs with r² between common and common SNPs (cc), low frequency and common SNPs (rc), and low frequency and low frequency SNPs (rr) in five intervals of r² within each category of the MAF of SNPs (i.e., cc, rc and rr categories) for low coverage pilot dataset. We plotted graphs under three inter-marker distances, A) 50 kb, B) 100 kb and C) 200 kb where r² between the target SNP and its all nearby SNPs within the distance was calculated.