Figure 1

Schematic overview of our method for detecting non-reference gene retrocopy insertions from paired read mappings. Read pairs are represented by two boxes for the sequenced portion of the paired read, joined by a line representing the unsequenced region (not to scale). Reads aligning to exonic sequences are colored red, and boxes aligning to non-exonic sequences are colored blue. For genomic intervals with no significant structural changes relative to the reference, reads will map normally as depicted in the upper panel. Note the forward-reverse orientation pattern of the read pair mappings as indicated under the sequenced ends. Non-reference gene retrocopy insertions (bottom panel) are represented by a series of discordant read mappings in a common interval (blue boxes) where one end of each read matches a distal exon on a common gene annotation (red boxes). The minimum interval between the left and right groups of blue boxes defines the start and end coordinates used in Additional file 1: Tables S2, S4-6, and S9. For Illumina paired reads, the forward-reverse sequencing scheme means that the non-exonic end of paired reads spanning the 5' junction is mapped in the forward orientation and the non-exonic read of the pair spanning the 3' junction is mapped in the reverse orientation (see arrows). Thus, the regions joined by oriented paired reads between reference chrB and the gene on reference chrA form a path that indicates a gene retrocopy insertion on the chrB allele in the individual genome from which the paired reads were derived. As depicted on the non-reference version of chrB, processed gene retrocopies lack introns, and the resulting exon-exon junctions are detectable by local assembly.