Fig. 2

Computational data analyses pipeline. a BLAST-based SVA Read filtering. Location of the 40 bp BLAST query sequence in the Alu-like region in the SVA Read is labelled. The two pair-end sequencing reads are represented by red arrow (SVA Read) and blue arrow (Flanking Read), respectively. b Flanking Read mapping and clustering. After mapping by BWA-MEM, Flanking Reads are filtered based on mapping quality score. Filtered Flanking reads that are within a 500 bp sliding window are then clustered into candidate insertion positions. The color scheme is same as Fig. 1. Black box: clustering window. c Identifying different types of SVA insertions. A representative genomic region (dark green box) is shown. Top row: SVA insertions identified by ME-Scan-SVA. Bottom row: known SVA annotated in the reference genome. Red star: fixed SVA insertions in the reference genome; blue star: known polymorphic SVA insertions