The relationship between LD and the transition:transversion ratio. In this figure, the solid black line plots the fraction of SNP pairs in LD that consist of two transitions. The fraction increases quickly as a function of the distance L between SNPs, asymptotically approaching the fraction of SNP pairs not in LD that consist of two transitions (solid gray line). The fraction of SNP pairs not in LD that consist of two transitions is nearly constant as a function of L except for an excess of adjacent transition pairs resulting from double mutation at CpG sites. Although transversion pairs make up just over 10% of unlinked SNP pairs, they account for >40% of adjacent SNPs in perfect LD and ∼20% of SNPs in LD at a distance of 10 bp apart.
