Table 1.

Chromosome 1 Bis-SNP detection

Sample	Aligner	reference	cvg	Het SNPs	Hom SNPs	Callable bases	runtime
OTB	MAQ	hg18	32×	119,103	67,725	211,042,010	2.8 h
TCGA-lung-normal	BSMAP	hg19	19×	118,412	58,309	222,763,786	3.1 h
TCGA-breast-normal	BSMAP	hg19	19×	113,009	57,281	221,014,965	2.7 h
Mouse-F1i	Novoalign	mm9	50×	663,528	65,364	178,718,615	3.1 h
Mouse-F1r	Novoalign	mm9	41×	682,979	67,068	178,847,508	3.1 h

Notes: All benchmarking performed using a single Intel(R) Xeon (X5650,2.67 GHz) server with 12 CPU cores and 10 GB memory. SE refers to single-end sequencing and PE to paired-end.