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Ag3: The Anopheles gambiae 1000 Genomes Project phase 3 data resource
8 Feb 2021


The Anopheles gambiae 1000 Genomes Project (Ag1000G) is a collaborative project using whole-genome sequencing to study genetic variation and evolution in natural populations of mosquitoes in the Anopheles gambiae species complex.

This page provides an overview of the open data resources released as part of the third phase of the Ag1000G project, known as “Ag3” for short. The Ag3 data resource includes genome-wide single nucleotide polymorphism (SNP) calls, SNP haplotypes, copy number variant (CNV) calls, and associated data for 2,784 wild-caught mosquitoes collected from 19 countries, and a further 297 mosquitoes from 15 lab crosses.


All samples in Ag3 have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants. After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls will be made openly available for download and analysis.

  • Ag3 SNP – Single nucleotide polymorphism (SNP) calls
  • Ag3 CNV – Copy number variant (CNV) calls
  • Ag3 Hap – SNP haplotypes

The Ag3 user guide is a useful companion to these data providing detailed information about the data, how to access and analyse in the cloud using free interactive computer services and Jupyter Notebooks.

Access the Ag3 user guide


Terms of use

Data from Ag3 are released openly and can be downloaded and analysed for any purpose. The data have been released prior to publication by the Ag1000G Consortium, and are currently subject to a publication embargo described further in the Ag1000G terms of use. If you have any questions about the terms of use, please email

Contributing studies

The Ag1000G project is coordinated by a consortium of partners from a range of different research institutions and countries. This includes consortium members who are carrying out independent research studies in malaria-endemic regions, and who have contributed mosquito specimens or mosquito DNA samples collected in the course of their own research. In total, 26 studies contributed samples to Ag3, including wild-caught specimens from 19 countries.

For further information about these contributing studies, the researchers involved, and the collection sites and methods, please see the contributing studies document.