Fig. 1

Computational detection of Alu insertion polymorphisms using split-reads. Alu insertions were identified using sequencing reads spanning the Alu integration locus whether these split-reads spanned the 5′ (a and c) or the 3′ (b and d) end of the insertion. The four split-reads represented in this figure are labeled a, b, c, and d. Green boxes represent Alu sequence; gray boxes denote flanking sequence. If the split-read is paired and its read-pair mapped to the flanking sequence (b and c), these mapping coordinates were used to provide additional support for the location predicted by the split-read. If the split-read’s read-pair mapped to the Alu (a and d), this was used to provide additional support for the presence of the predicted Alu insertion