Fig. 4
Two examples of groups of SNPs with alleles in linkage disequilibrium r2 = 1. Both examples contain SNPs across the chromosome (core and prophage regions) and plasmids. (A) is a collection of SNPs in LD across all 181 samples both within the chromosome and pO157 plasmid. (B) is a collection of SNPs specific to clade 2 (stx1a stx2c) and demonstrates a collection of alleles in LD both within the chromosome and within a plasmid common to the clade. Note that both examples have SNPs within both the core and prophages regions of the chromosome