Reads identified as correctly and incorrectly mapped. Two representative alignments of simulated reads (read 1 and read 2). produced by a mapper in the special case of indels in homopolymers at the end of an alignment. In each case, the first alignment is the expected alignment for the simulated read with the correct number of insertions, deletions, and substitutions; the second alignment is the alignment returned by a mapper.
Caboche et al. BMC Genomics 2014 15:264 doi:10.1186/1471-2164-15-264