Percentage of mapped and correctly mapped reads with different programs: a) BLAT, b) SSAHA2, c) Bowtie, d) SeqMap, e) MAQ, g) CLC NGS Cell.

In each simulation the labels for each bar indicate in the order: organism (y = S. cerevisiae, d = D. melanogaster, a = A. thaliana, h = H. sapiens), mapping against the transcriptome (t) or the genome (g), read length (35 bp, 50 bp, 100 bp).