Mapping results of the three mappers with short reads (length = 50 bps). (a) Mapping rate of the three mappers across read error rates. The mapping rate was calculated as mapped read number over total read number. (b) Mapping accuracy of the three mappers across read error rates. The mapping accuracy was calculated as the rate of correctly mapped read number over mapped read number. Mapping rate (c) and mapping accuracy (d) of the three mappers within all of hg19 chr19, LINEs, and SINEs. In this case, the read error rate was 2%. Mapping accuracy of the three mappers with reads in which error rate equals to 2% (e) and 8% (f). X-axis means methylation level in reads set at the bisulfite-read generation step. (g) Percentage of Ts in each read that were (in)correctly mapped by the three mappers.