Fig. 3
ALVE21 genotyping and identification of the WPR K locus revertant (kR). a IGV alignment view of the empty ALVE21 integration site in a FF WL. b IGV alignment view in the SF WPR. Base mismatches are coloured and show the split reads on either side of the TSD. Approximately 50% of reads align through the TSD, supporting the empty ALVE21 integration site in the tandem repeat of the K locus. c IGV alignment view in the FF WPR showing the ALVE21 integration, but with no reads aligning across the TSD. d ALVE21 KASP assay. All FF WPR individuals appear homozygous for ALVE21. All SF individuals appear heterozygous due to the empty site in the tandem repeat. e KASP assay for the unique bridging sequence between the two tandem repeats is only seen in the SF lines and not in any FF, including the FF WPR. Plot values corrected for representation of the internal control in all groups. f Optic maps generated across the K locus (coordinates show Mbp on the Z chromosome) using the Nt.BspQ1 restriction enzyme. The in silico shows predicted Nt.BspQ1 sites (vertical bars). Cases where predicted sites are very close (red circles) cannot be resolved beyond a single site. Predicted site dropout (open circle) may represent a mutation in that Nt.BspQ1 site. The WL-FF optic map matches the in silico exactly. The WPR-FF shows a ~ 7.5 kbp longer optic map representing the integrated ALVE21. Optic map figures were adapted from IrysView