Table 3. Overall detection sensitivities.

The total percentage of mutations detected post-alignment across the 67 groups of simulated Illumina reads was recorded for single and paired-end run-modes. Each read group contained 13 INDELs of varying sizes as well as 20 SNPs.

Aligner	Sensitivity PE	Sensitivity SE
BWA	99.23	94.53
Bfast	90.68	87.83
Smalt	98.55	98.51
Stampy	99.46	99.05
Mosaik	97.06	95.07
CLC	98.01	97.92
CLCBeta	96.88	96.74
Novoalign	99.59	99.00
Omixon	99.41	99.14
Bowtie2	98.91	98.19
Nextgene	98.64	98.69