Figure 2

Properties of methylC-seq coverage and spatial correlation of CpG methylation level. (A) Quantile-quantile (Q-Q) plot between observed coverage and theoretical coverage which is from a shifted negative binomial distribution. (B) Spatial correlation plot of a honeybee methylome from Herb et al. [7]. (C) Q-Q plot between observed p-values from Kolmogorov-Smirnov (K-S) test and theoretical p-values from a null distribution. The K-S test was used to detect the spatial correlation between selected CpG sets, consisting of one CpG per window. Detailed procedure is explained in the Additional file 1. The green region implies 95% confidence interval of theoretical ordered p-values. The overlap between the observed P-values indicates that the data follows the null distribution. (D) Spatial correlation plot of an Arabidopsis methylome (methylC-seq data from GSM276809, [29]). (E) Smoothed methylation level using triangle kernel in scaffold 1.1, for three samples. X-axis is physical location and Y-axis is methylation level. Red lines represent average methylation fractions calculated from whole CpG methylomes.