Figure 2

Junction candidate creation from split-read alignments that overlap. a) If two alignments of a read to the reference genome overlap, the overlapping bases at the center of the read could potentially be assigned to two separate locations in the reference sequence. b) If the read alignments in (a) had the imperfect alignments pictured here, the coordinates of each match and their overlap would be corrected as pictured by removing overlap until the remainder is a perfect match with no indels or mismatched bases. c) This type of junction candidate can be fully described by the reference coordinates defining each side of the junction breakpoint, the directions in the reference sequence each junction side continues to match from those breakpoint positions, and the number of overlapping bases in the read alignments.