Fig. 2

Computational data analysis overview. a) The paired-end sequencing reads. Sequencing reads from the pooled libraries are represented by red (ME Reads) and blue arrows (Flanking Reads), respectively. b) Read filtering. The ME Reads are compared to the targeted ME consensus to identify recent insertions and are filtered based on the BLAST bit-score cutoff. The Flanking Reads are mapped to the reference genome and are filtered based on the mapping quality score cutoff. c) Flanking Read clustering and insertion loci identification. Filtered Flanking reads that are within a 500 bp sliding window are clustered into a candidate insertion locus and the genomic position closest to the ME Read is selected as the insertion position (marked with a star). Black box: clustering window