Aligning a read that spans a fusion point. (a) An initially unmapped read of 75 bp is split into three segments of 25 bp, each of which is mapped separately. As shown here, the left (red) and right (blue) segments are mapped to two different chromosomes, i and j. (b) The unmapped green segment is used to find the precise fusion point between i and j. This is done by aligning the green segment to the sequences just to the right of the red segment on chromosome i and just to the left of the blue segment on chromosome j.