Simulations allow estimation of the overall fraction of single nucleotide polymorphisms (SNPs) across the genome with differential local methylation. (a) Under different simulations, we calculated the sum of squares of fractional deviations of the simulated data compared with empirical data examining fractional differences in four parameters: methylation overlap, opposite overlap and methylation overlap in three individuals, and methylation overlap in four individuals. (b) The fractions of amplicons showing methylation overlap in groups of two, three and four individuals for observed (Obs.), expected (Exp.) and simulated (Sim.) data.