Mapping against fusion points and selecting best read alignments. (a) Bowtie is used to align all segments from the initially unmapped (IUM) reads against spliced fusion contigs, shown in gray on the right. For example, the brown read on the top left aligns to the first spliced fusion contig on the top right. (b) IUM reads 1 and 2 each have multiple alignments. Read 1 has a gap-free alignment, shown in dark blue, which is preferred over the other two alignments shown in lighter shades of blue. The gap-free alignment with three mismatches is preferred over the fusion alignment with one mismatch. If all alignments have gaps and mismatches, then the algorithm prefers those with fewer mismatches, as shown by the dark green alignment for IUM read 2. Full details of the scoring function that determines these preferences are described in the Materials and methods.