Table 1. Summary of the alignment accuracies achieved by MOSAIK for reads generated from different sequencing technologies.

Technologies	Aligned (%)	Speed (reads/second)	Read lengths [min;max]	Reference genome	Dataset
Illumina; PE	99.98	83.95	100; 50	Human hg19	MASON simulated
Illumina; SE	99.75	153.98	100; 76; 50	Human hg19	MASON simulated
Illumina; PE/SE	91.48	147.42	81; 76; 51; 45; 41	Human hg19	CHB population in 1000G
454; SE	99.42	8.018	400.673 [266;529]	Human hg19	MASON simulated
Ion Torrent	77.02	20.85	223.99 [59;398]	E. coli strain 536	Ion Torrent released
SOLiD	55.64	126.81	50	Human hg19	CHB population in 1000G
Pacific Biosciences*	85.79	0.69	698.61 [48;6084]	V. cholerae 4,033,464 bp.	Pacific Biosciences released

*The parameter set “-hs 10 -mmp 0.5 -act 15” was used as opposed to the default values “-hs 15 -mmp 0.15 -act 55”.

With the exception of the Pacific Biosciences data, all alignments were generated using MOSAIK's default parameters.