Figure 2.

Effect of CpG variation on global methylation. (A) Global methylation estimated for four samples each of two different mouse strains (BL6 and CAST) aligned to either of the two reference genomes. Samples aligned to the strain-specific genome display higher global methylation compared to the same sample aligned to a distant reference genome. (B) Average methylation for different subsets of CpGs within BL6 and CAST samples, all aligned to the BL6 reference genome. In CAST samples, CpGs unique to BL6 are quantified as having 0% methylation.