Relationship between genetic and methylation divergence in each sequence contexts. The average number of nucleotide differences per site (indicated by x-axis) and average Spearman correlation coefficients (r) of methylation level of all cytosines among samples (indicated by y-axis) were calculated for each 50-kb sliding window with a step of 25 kb across the whole genome. Then all sliding windows were classified into 20 groups with equal numbers (657 sliding windows) according to their π values from the lowest to the highest. The average number of nucleotide differences per site and r of each group were calculated and their values were plotted. Because most sliding windows have relatively small values of average number of nucleotide differences per site, the data points in the figure were enriched in the left.