A Distribution of the number of cytosines per context for regions vs. 100 bp bins. The median for regions is 8, 9, and 31 for CG, CHG, and CHH. Median numbers per bin are 4, 5, and 26. B Distribution of the density of cytosines per context in regions vs. 100 bp bins. The median for regions is 0.11 for CG, 0.10 for CHG, and 0.30 for CHH, while for bins it is 0.04, 0.05, and 0.26. The modality of C density in regions is caused by Singlets and Duplets, which consist of 1–3 Cs in 1–3 bps. C Percentages of annotations overlapping with regions per context. The dots represent the percentages of single cytosines. D Mean methylation levels and E standard deviation per region for all MA lines, colored by whether they were called methylated, unmethylated, or intermediate.