Table 2. The positive predictive values (the number of correctly mapped reads divided by the total number of mapped reads) in terms of mapping quality cutoffs.

MQ cutoffs	30		20		10		0
Read lengths	100	76	100	76	100	76	100	76
BWA	1	1	0.9998	0.9997	0.9996	0.9995	0.9971	0.9959
BOWTIE	0.9998	0.9992	0.9982	0.9976	0.9980	0.9972	0.9823	0.9819
STAMPY	0.9961	0.9986	0.9945	0.9982	0.9897	0.9954	0.9813	0.9909
MOSAIK	1	1	1	1	0.9999	0.9999	0.9962	0.9947