Fig. 3

WGS (track a) and WES (track b) alignments over a 722 bp region on CANFA33 from a PRA-affected LA compared to control WGS data from a PRA-unaffected Hungarian Vizsla dog (example, track c). The identified LINE-1 insertion is upstream of the retinal candidate gene IMPG2. Grey sequencing reads show those aligning normally to the CanFam3.1 canine reference genome at this position. Coloured reads indicate that one of the paired sequencing reads aligns to this region on CANFA33, and the mate in this pair of sequencing reads aligns to another chromosome (each colour represents alignment to a different chromosome), consistent with the presence of a repetitive element insertion