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Table 1 Mapping 1M synthetic human chr. 21 reads onto human chr. 21

From: BS Seeker: precise mapping for bisulfite sequencing

Aligner Experimental protocol Uniquely (or besta) mapped readsb(%) Accuracy (%) Methylation ratesc(CG/CHG/CHH) (%) CPU time
No base calling error       
BS Seeker Lister et al 91.7 100 72.0 0 0 209 s d
BSMAP Lister et al 92.1 100 72.3 0 0 15h43m20s
RMAP Lister et al 91.7 100 72.0 0 0 185 s
MAQ Lister et al >99.9 93.4 67.7 0 0 353 s
BS Seeker Cokus et al 89.6 100 72.0 0 0 263 s d
BSMAP Cokus et al 89.8 99.6 72.4 0 0 15 h 46 m 40 s
RMAP Cokus et al 80.2 99.0 71.3 0 0.1 400 s
MAQ Cokus et al 73.0 92.2 68.2 0 0 665 s
Simulated base calling errors       
BS Seeker Lister et al 91.2 99.54 71.5 0.4 0.4 217 s
BSMAP Lister et al 91.1 99.57 72.1 0.4 0.4 15 h 19 m 51 s
RMAP Lister et al 91.0 99.52 71.6 0.4 0.4 188 s
MAQ Lister et al 99.5 92.9 67.8 0.4 0.4 340 s
  1. a BS Seeker, BSMAP, and RMAP discard non-uniquely mapped reads. MAQ keeps non-uniquely mapped reads and assigns them to one of the best-matching positions. b Up to 2 mismatches are allowed. c The simulated methylation rates are set to be 72%, 0%, and 0% for CG, CHG, and CHH. d Preprocessing reference genome needs 2-5 cpu minutes for the first run.