(A) The number of cytosines in the methylated and unmethylated state for the nuclear and chloroplast genome. (B) The proportion of mCGs, mCHGs, and mCHHs in the VC1973A genome. (C) DNA sequence logo plot of the methylated cytosine contexts. (D) Density plots of the weighted methylation levels for mCG, mCHG, and mCHH. (E) Average methylation levels for gene bodies and their flanking regions. (F) The distribution of methylated cytosine counts in 50 Kb windows of chromosome 1.