Genotypes of Aedes aegypti mosquitoes derived from SNP chip and low-coverage whole genome sequencing for platform cross-validation

The mosquito Aedes aegypti is the primary vector of many human arboviruses such as dengue, yellow fever, chikungunya, and Zika, which affect millions of people world-wide. Population genetics studies on this mosquito have been important in understanding its invasion pathways and success as a vector of human disease. The Axiom aegypti1 SNP chip was developed from a sample of geographically diverse Ae. aegypti populations to facilitate genomic studies on this species. Here we evaluate the utility of the Axiom aegypti1 SNP chip for population genetics and compare it with a low-depth shot-gun sequencing approach using mosquitoes from the species’ native (Africa) and invasive range (outside Africa). These analyses indicate that the results from the SNP chip are highly reproducible and have a higher sensitivity to capture alternative alleles than a low-coverage whole-genome sequencing approach. Although the SNP chip suffers from ascertainment bias, results from population structure, ancestry,..., DNA from individual Aedes aegypti mosquitoes was extracted and used for genotyping at 50,000 loci distributed along the species genome, using the Axiom Aegypti1 SNP chip (Life Technologies Corporation CAT#550481). 
Files \"all_snps_G3Dryad\" and \"Replicas_SNPchip\" contain all 50,000 SNPs genotyped, prior to filtering. 
File \"50k_SNPs_30_samples_LD_MAF_miss_FINAL\" contain the SNPs after applying filters in Plink 1.9 (https://www.cog-genomics.org/plink/) for linkage disequilibrium (LD: -indep-pairwise 50 10 0.3), minor allele frequency (MAF: -maf 0.1) and missing data (-geno 0.1)., , # Genotypes of Aedes aegypti mosquitoes derived from SNP chip and low-coverage whole genome sequencing for platform cross-validation

[https://doi.org/10.5061/dryad.m0cfxppbd](https://doi.org/10.5061/dryad.m0cfxppbd)

Files: Replicas_SNPchip

SNP chip data generated from 20 individual *Aedes aegypti* mosquitos from Sudan and Sri Lanka using the Axiom Aegypti1 array (Life Technologies Corporation CAT#550481) . Each mosquito was genotyped in triplicate independently in different chips. All 50,000 loci genotyped are included, prior to any filtering.

Files: all_snps_G3Dryad

SNP chip data generated from 13 individual *Aedes aegypti* mosquitos from populations worldwide using the Axiom Aegypti1 array (Life Technologies Corporation CAT#550481). All 50,000 loci genotyped are included, prior to any filtering.

File: 50k_SNPs_30_samples_LD_MAF_miss_FINAL.vcf.gz

Variant calling file (vcf) containing 30 individual *Aedes aegypti *genotypes used for population genetic analysis, with five individu...,