Fig. 3

Comparison of methylation levels between EM-seq and WGBS. a–d Boxplots showing whole-genome CG (a), CHG (b), CHH (c), and C (d) methylation levels in EM-seq and WGBS. WGBS libraries prepared with 18 PCR cycles are indicated with brackets in the boxplots. Blue boxes represent EM-seq and red boxes represent WGBS. The P values, shown at the top of the plots, were estimated using a Student’s t-test. e Boxplots showing the relationship between methylated CG, methylated CHG, and methylated CHH counts (x-axis) and methylation levels (y-axis) in WGBS and EM-seq. f Methylation differences (average WGBS methylation levels minus average EM-seq methylation levels) from e. In e and f, for CG methylation, only regions with even numbers of CG sites have been analyzed, since CG methylation is symmetrical