Table 5. Raw numbers of false positive and negative mutations detected across 67 groups of simulated Illumina reads following alignment with each aligner in single and paired-end mode.

Each read group contained 20 SNPs and 13 INDELs.

Aligner	# False positives PE	# False positives SE	# False negatives PE	# False negatives SE
BWA	23	168	17	121
Bfast	884	759	206	269
Smalt	10	14	32	33
Stampy	263	95	12	21
Mosaik	314	76	65	109
CLC	21	23	44	46
CLCBeta	119	566	69	72
Novoalign	6	10	9	22
Omixon	39	21	13	19
Bowtie2	249	66	24	40
Nextgene	395	117	30	29