Number of SNP effects by genomic region. Variant effects were categorized using SNPEff  based on their position in the annotated Aedes aegypti genome. These include: introns, exons, untranslated region (5’ UTR and 3’ UTR), splice site or intergenic regions. “Upstream” is defined as a region 5 kilobase (kb) upstream of the most distal transcription start site and “downstream” as 5 kb downstream of the most distal polyA addition site . Because some SNPs found between closely positioned genes were categorized as both upstream and downstream effects, the total number of effects was greater than the total number of SNPs.