Filtering reads with incomplete bisulfite conversion. (A) Distribution of the unconverted ratio of CH sites (H = A, C, T) in phage DNA reads which has at least one CH site unconverted. Phage DNA is free of DNA methylation and used as a control. The distribution chart indicates two different categories: sporadic (red) and dense (blue) methylation. BS-Seeker2 provides an option for removing reads with dense non-CpG methylation. (B) Filtering un-converted reads makes the methylation levels of two technical replicates more similar. Error bar, SD.