CG-DMRs (Fig. 3) were identified similarly to non-CG mega-DMRs. Smoothed average methylation level was performed in 100-bp windows sW, and regions comprising a set of 10 adjacent windows sW over a distance less than 1,100 bp were considered. The Kruskall–Wallis test was used to score each region based on the methylation levels from the two ES cell and five iPSC lines. Regions with corrected P value, < 0.01 (1% FDR) and 4-fold enrichment of methylation level (max/min over the 7 cell lines for each region) were identified, and regions closer than 100 bp were joined, resulting in a final set of 1,175 CG-DMRs. Regarding the H1 versus H9 comparison, the non parametric Wilcoxon test was applied: at 1% FDR and minimum 4-fold enrichment no CG-DMRs could be identified, while only at 10% FDR and 4-fold enrichment could H1 versus H9 CG-DMRs be identified. This 10% FDR set has an overlap of 131 kb with the final set of 1,175 CG-DMRs. For these reasons the set of DMRs that visually appear different between H1 and H9 in the Fig. 3 heatmap
