Nucleotide diversity within the female-specific exon 5 of the doublesex gene (dsx; AGAP004050), a key component of the sex determination pathway and a gene targeted for Cas9-based homing endonuclease gene drive (Kyrou et al. 2018). In both plots, the location of exon 5 within the female-specific isoform (AGAP004050-RB; AgamP4.12 gene set) is shown above (black indicates coding sequence; gray, untranslated region), with additional annotations above to show the location of Cas9 target sequences containing at most one SNP, and the putative exon splice enhancing sequences (“RE”) reported by Scali et al. (2005). The main region of the plot shows nucleotide diversity averaged across all Ag1000G phase 2 populations, computed in 23-bp moving windows. Regions shaded pale red indicate regions not accessible to SNP calling. Triangle markers below show the locations of SNPs discovered in Ag1000G phase 2 (green indicates passed variant filters; red, failed variant filters). (A) exon5/intron4 boundary. (B) exon5/intron6 boundary.
