Comparison of the sensitivity between FANSe and Bowtie by mapping of in silico simulated datasets. ( A ) Sensitivity of mapping indel-free reads from the E. coli genome and masked human chromosome 21 reference sequence. FANSe was run with 6-nt seeds. ( B ) Sensitivity of mapping reads from the E. coli genome with a 1% substitution rate and an indel rate ranging from 0.5% to 4%. Indel search is enabled. All tests with Bowtie were run with three mismatch allowance. MM, mismatches.