100 k reads of length 50 bp are simulated from the RR genome. Mapping is done using BS-Seeker2 (Bowtie). Mapping to the reduced represented (RR) index is much faster than mapping to the whole genome (WG) index. For error-free samples, the mappability to RR is higher than WG by avoiding pseudo-multiple hits. For error-containing samples, mapping to the RR index will result in higher accuracy than mapping to the WG index. Arrows indicate the improvement directions.