Ag3.7#

The Ag3.7: Anopheles gambiae data resource contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 2546 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 Ag3.7.

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 17th of November 2025.

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

Partner studies#

1190-VO-GH-AMENGA-ETEGO - Population genetics, parasite diversity and ecology of the major malaria vectors in the Kassena-Nankana Districts of Ghana
1237-VO-BJ-DJOGBENOU - Genomics for African Anopheles Resistance Diagnostics/GAARDian (Benin)
1246-VO-TZ-KABULA - Genome-based diagnostics for monitoring and evaluation of insecticide resistance in Anopheles gambiae in Tanzania
1270-VO-MULTI-PAMGEN - Pan-African Malaria Genetic Epidemiology Network (PAMGEN) Anopheles gambiae samples (Cameroon)
1281-VO-CM-CHRISTOPHE - PAMCA Anopheles genomics programme - Malaria vector surveillance, population genetics and insecticide resistance characterization in four eco-epidemiological settings in Cameroon

This release also includes data from 2 studies openly available in the literature: barron-2019 and crawford-2016.

Whole-genome sequencing and variant calling#

All samples in Ag3.7 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 Ag3.7 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 MyBinder and 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 Ag3.7 have been organised into 9 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
1190-VO-GH-AMENGA-ETEGO	1190-VO-GH-AMENGA-ETEGO-VMF00088	255
1190-VO-GH-AMENGA-ETEGO	1190-VO-GH-AMENGA-ETEGO-VMF00102	273
1237-VO-BJ-DJOGBENOU	1237-VO-BJ-DJOGBENOU-VMF00212	451
1246-VO-TZ-KABULA	1246-VO-TZ-KABULA-VMF00185	467
1246-VO-TZ-KABULA	1246-VO-TZ-KABULA-VMF00197	327
1270-VO-MULTI-PAMGEN	1270-VO-MULTI-PAMGEN-VMF00193-VMF00202	276
1281-VO-CM-CHRISTOPHE	1281-VO-CM-CHRISTOPHE-VMF00208	468
barron-2019	barron-2019	4
crawford-2016	crawford-2016	25

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	fontenillei	gambiae	gcx4	melas	unassigned
study_id	sample_set	country	year
1190-VO-GH-AMENGA-ETEGO	1190-VO-GH-AMENGA-ETEGO-VMF00088	Ghana	2018	2	246	0	6	0	0	1
1190-VO-GH-AMENGA-ETEGO	1190-VO-GH-AMENGA-ETEGO-VMF00102	Ghana	2018	2	268	0	3	0	0	0
1237-VO-BJ-DJOGBENOU	1237-VO-BJ-DJOGBENOU-VMF00212	Benin	2018	0	380	0	21	0	50	0
1246-VO-TZ-KABULA	1246-VO-TZ-KABULA-VMF00185	Tanzania	2018	467	0	0	0	0	0	0
1246-VO-TZ-KABULA	1246-VO-TZ-KABULA-VMF00197	Tanzania	2019	97	0	0	227	0	0	3
1270-VO-MULTI-PAMGEN	1270-VO-MULTI-PAMGEN-VMF00193-VMF00202	Cameroon	2020	0	69	0	173	0	0	1
1270-VO-MULTI-PAMGEN	1270-VO-MULTI-PAMGEN-VMF00193-VMF00202	Cameroon	2021	0	24	0	5	0	4	0
1281-VO-CM-CHRISTOPHE	1281-VO-CM-CHRISTOPHE-VMF00208	Cameroon	2019	8	173	0	85	0	0	0
			2020	1	25	0	16	0	0	0
			2021	13	52	0	95	0	0	0
barron-2019	barron-2019	Gabon	2014	0	0	4	0	0	0	0
crawford-2016	crawford-2016	Burkina Faso	2007	0	0	0	0	4	0	0
		Burkina Faso	2008	5	7	0	0	8	0	0
		Guinea	2012	0	0	0	1	0	0	0

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

MalariaGEN vector data user guide

Ag3.7

Contents