Table 6. Positive predictive values (PPVs) calculated for each aligner in single and paired-end mode based upon downstream detection of mutations across 67 groups of simulated Illumina reads each containing 20 SNPs and 13 INDELs.

In this case PPV is the total number of true positives divided by the sum of the total number of true positives and true negatives.

Aligner	PPV PE	PPV SE
BWA	98.96	92.56
Bfast	69.40	71.90
Smalt	99.54	99.36
Stampy	89.32	95.84
Mosaik	87.24	96.51
CLC	99.04	98.95
CLCBeta	94.74	79.08
Novoalign	99.73	99.55
Omixon	98.26	99.05
Bowtie2	89.78	97.05
Nextgene	84.67	94.91