Comparison between MOABS and FETP in detecting DMCs. We simulated 1,000,000 CpGs in two samples with predefined true positive or true negative states. In both samples, 900,000 true negative CpGs were initially assigned the same methylation ratios. The density of the methylation ratios fits a bimodal distribution (Additional file 3: Figure S1) frequently observed in real BS-seq data. The remaining true positive 100,000 CpGs were randomly assigned at low ratios [0, 0.25] in one sample and high ratios [0.75,1] in the other sample, respectively. Each methylation ratio was then given a +/-0.05 fluctuation to simulate BS-seq errors. Sequencing depth is randomly sampled from 5-fold to 50-fold. The Y-axis shows the percentage of true DMCs predicted at 5% FDR.