This repository contains two VCF files that were generated from the called genotyped obtained from ANGSD. One VCF file contains variants obtained from whole-genome sequencing data from one individual sample of Aedes bromeliae (aedesBromeliae__1sample__Brom.mdp8.vcf.gz ) The other VCF file contains variants obtained from whole-exome sequencing data from 71 individual samples belonging to different populations in Africa and outside of Africa (aedesAegypti__71samples__AEGY.allpop.J18.AllSites.REFpol.CALLED.vcf_.gz). The data is accompanied by the raw sequencing data available in SRA with the accession number SRP092518 and with the BioProject number PRJNA349448 More information about the project is available in the manuscript that is under preparation. ; ERC [Drosophila Infection (281668) to Francis M. Jiggins], MRC Centenary Award to William J Palmer, National Institutes of Health Ruth L. Kirschstein National Research Service Award to Jacob Crawford, KAUST AEA award to Francis M. Jiggins and Arnab Pain