Ag3.9

The Ag3.9: Anopheles gambiae data resource contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 3639 mosquitoes.

More information about this release can be found in the data resource website.

This page provides an introduction to open data resources released as part of Ag3.9.

If you have any questions about this guide or how to use the data, please start a new discussion on the malariagen/vector-open-data repo on GitHub. If you find any bugs, please raise an issue.

Terms of use

Data from this project will be made publicly available before journal publication. Unless otherwise stated, analyses of project data are ongoing and publications are in preparation by project partners, and it is not permitted to use project data for publication (including any type of communication with the general public) without prior permission from the originating partner studies.

Although malaria is generally an endemic rather than an epidemic disease, and the focus of this project is on surveillance of disease vectors rather than pathogens, our data terms of use build on MalariaGEN’s approach to data sharing, and adopt norms which have been established for rapid sharing of pathogen genomic data during disease outbreaks. The primary rationale for this approach is that malaria remains a public health emergency, where ethically appropriate and rapid sharing of genomic surveillance data can help to detect and respond to biological threats such as new forms of insecticide resistance, and to adapt malaria vector control strategies to different settings and changing circumstances.

The publication embargo for all data on this release will expire on the 9th of April 2026.

If you have any questions about the terms of use, please email support@malariagen.net

Partner studies

• 1270-VO-MULTI-PAMGEN (Ethiopia) - PAMGEN: Genetic interactions between human populations and malaria parasites in different environmental settings across Africa

• 1270-VO-MULTI-PAMGEN (The Gambia) - PAMGEN: Genetic interactions between human populations and malaria parasites in different environmental settings across Africa

• 1274-VO-KE-KAMAU - PAMCA Anopheles genomics programme - Anopheles gambiae and Anopheles arabiensis genetic diversity and association with insecticide resistance in Kenya

• 1280-VO-ZA-MUNHENGA - PAMCA Anopheles genomics programme - Genetic structuring in the major malaria vector Anopheles arabiensis and implication on vector control in South Africa

• 1281-VO-CM-CHRISTOPHE - ANOSPP screening of Anopheles species and Plasmodium presence in malaria vectors in Nigeria

• 1323-VO-GM-NGWA - Anopheles gambiae vector surveillance in The Gambia

• 1329-VO-GA-CHRISTOPHE - PAMCA Anopheles genomics programme - Anopheles gambiae vector surveillance in Gabon

This release also includes data from two studies openly available in the literature:

• campos-2021 - The origin of island populations of the African malaria mosquito, Anopheles coluzzii & Selection of sites for field trials of genetically engineered mosquitoes with gene drive.

• bergey-2019 - Assessing connectivity despite high diversity in island populations of a malaria mosquito.

Whole-genome sequencing and variant calling

All samples in Ag3.9 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 such as single nucleotide polymorphisms (SNPs). 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 are openly available for download and analysis.

For further information about the sequencing and variant calling methods used, please see the methods page.

Data hosting

Data from Ag3.9 are hosted by several different services.

The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as Google Colab. Further information about analysing these data in the cloud is provided in the cloud data access guide.

Sample sets

The samples included in Ag3.9 have been organised into 6 sample sets.

Each sample set corresponds to a set of mosquito specimens from a contributing study. Study details can be found in the partner studies webpages listed above.

	sample_set	sample_count
study_id
1270-VO-MULTI-PAMGEN	1270-VO-MULTI-PAMGEN-VMF00218	273
1270-VO-MULTI-PAMGEN	1270-VO-MULTI-PAMGEN-VMF00232	212
1274-VO-KE-KAMAU	1274-VO-KE-KAMAU-VMF00246	564
1280-VO-ZA-MUNHENGA	1280-VO-ZA-MUNHENGA-VMF00222	223
1281-VO-CM-CHRISTOPHE	1281-VO-CM-CHRISTOPHE-VMF00227	59
1323-VO-GM-NGWA	1323-VO-GM-NGWA-VMF00235	188
1323-VO-GM-NGWA	1323-VO-GM-NGWA-VMF00242	1630
1329-VO-GA-CHRISTOPHE	1329-VO-GA-CHRISTOPHE-VMF00228	146
bergey-2019	bergey-2019	113
campos-2021	campos-2021	163

Here is a more detailed breakdown of the samples contained within this sample set, summarised by country, year of collection, and species:

			taxon	arabiensis	coluzzii	gambiae	gcx1	gcx2	melas	merus	quadriannulatus	unassigned
study_id	sample_set	country	year
1270-VO-MULTI-PAMGEN	1270-VO-MULTI-PAMGEN-VMF00218	Ethiopia	2021	273	0	0	0	0	0	0	0	0
	1270-VO-MULTI-PAMGEN-VMF00232	Gambia, The	2019	166	4	10	1	28	0	0	0	3
1274-VO-KE-KAMAU	1274-VO-KE-KAMAU-VMF00246	Kenya	2006	19	5	1	0	0	0	0	0	0
			2007	18	0	0	0	0	0	0	0	0
			2013	24	0	4	0	0	0	0	0	0
			2014	15	0	0	0	0	0	0	0	0
			2019	305	21	32	0	0	0	0	2	0
			2020	72	0	0	0	0	0	0	0	0
			2021	45	0	0	0	0	0	0	1	0
1280-VO-ZA-MUNHENGA	1280-VO-ZA-MUNHENGA-VMF00222	South Africa	2021	99	0	0	0	0	0	0	0	0
			2022	122	0	0	0	0	0	1	1	0
1281-VO-CM-CHRISTOPHE	1281-VO-CM-CHRISTOPHE-VMF00227	Cameroon	2020	0	1	58	0	0	0	0	0	0
1323-VO-GM-NGWA	1323-VO-GM-NGWA-VMF00235	Gambia, The	2005	65	0	0	1	18	24	0	0	0
			2014	1	0	0	0	0	0	0	0	0
			2021	6	1	1	38	32	0	0	0	1
	1323-VO-GM-NGWA-VMF00242	Gambia, The	2019	683	12	41	49	552	265	0	0	28
1329-VO-GA-CHRISTOPHE	1329-VO-GA-CHRISTOPHE-VMF00228	Gabon	2020	1	0	144	0	0	0	0	0	1
bergey-2019	bergey-2019	Uganda	2015	0	0	113	0	0	0	0	0	0
campos-2021	campos-2021	Angola	2010	0	8	0	0	0	0	0	0	0
		Benin	2014	0	11	0	0	0	0	0	0	0
		Cameroon	2003	0	4	0	0	0	0	0	0	0
			2011	0	4	0	0	0	0	0	0	0
		Comoros, The Union of the	2011	0	0	35	0	0	0	0	0	0
		Equatorial Guinea	2002	0	5	4	0	0	0	0	0	0
		Gabon	2018	0	5	0	0	0	0	0	0	0
		Guinea-Bissau	2009	0	0	0	6	8	0	0	0	0
		Madagascar	2018	0	0	10	0	0	0	0	0	0
		Mali	2002	0	2	0	0	0	0	0	0	0
			2004	0	5	0	0	0	0	0	0	0
			2006	0	3	6	0	0	0	0	0	0
			2010	0	2	0	0	0	0	0	0	0
			2012	0	2	0	0	0	0	0	0	0
		Sao Tome and Principe	1998	0	12	0	0	0	0	0	0	0
			2017	0	19	0	0	0	0	0	0	0
		Tanzania	2012	0	0	6	0	0	0	0	0	0
		Zambia	2015	0	0	6	0	0	0	0	0	0

Note that there can be multiple sampling sites represented within the same sample set.

Further reading

We hope this page has provided a useful introduction to the Ag3.9 data resource. If you would like to start working with these data, please visit the cloud data access guide or the data download guide or continue browsing the other documentation on this site.

If you have any questions about the data and how to use them, please do get in touch by starting a new discussion on the malariagen/vector-data repository on GitHub.