Additional file 4.

Comparison of context bias after removing CpG-containing patterns. One possible explanation for observed differences in context bias is that the methylation process that produces biases at 2 bp is also influenced by context at larger scales. To address this, we calculated context bias for each data set in Figure 2 while excluding substitution patterns including an ancestral CpG. We find that the effects at 3-5 bp remain, which suggests that bias at these scales is not working via the rate of cytosine deamination at CpG sites.

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Nevarez et al. BMC Bioinformatics 2010 11:462   doi:10.1186/1471-2105-11-462