Ag3.10#

The Ag3.10: Anopheles gambiae data resource contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 1164 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 Ag3.10.

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 24th of June 2026.

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

Partner studies#

This release also includes data from one study openly available in the literature:

Whole-genome sequencing and variant calling#

All samples in Ag3.10 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 Ag3.10 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 Ag3.10 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
1188-VO-SN-NIANG 1188-VO-NIANG-NIEL-SN-2304-VMF00259 660
1270-VO-MULTI-PAMGEN 1270-VO-MULTI-PAMGEN-VMF00244 252
1330-VO-GN-LAMA 1330-VO-GN-LAMA-VMF00250 180
fontaine-2015-rebuild fontaine-2015-rebuild 72

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 melas merus quadriannulatus unassigned
study_id sample_set country year
1188-VO-SN-NIANG 1188-VO-NIANG-NIEL-SN-2304-VMF00259 Senegal 2017 0 0 0 0 1 0 0 0
2020 94 42 149 4 31 0 0 8
2021 9 32 8 1 0 0 0 5
2022 173 62 21 17 0 0 0 3
1270-VO-MULTI-PAMGEN 1270-VO-MULTI-PAMGEN-VMF00244 Mali 2021 28 96 48 0 0 0 0 0
2022 0 75 5 0 0 0 0 0
1330-VO-GN-LAMA 1330-VO-GN-LAMA-VMF00250 Guinea 2022 0 164 16 0 0 0 0 0
fontaine-2015-rebuild fontaine-2015-rebuild Burkina Faso 2004 4 0 0 0 0 0 0 0
2012 0 3 4 0 0 0 0 0
Cameroon 2005 4 8 8 0 0 0 0 0
2010 0 0 0 0 4 0 0 0
Kenya 1988 0 0 0 0 0 4 0 0
Mali 2004 0 0 10 0 0 0 0 0
South Africa 1988 0 0 0 0 0 5 0 0
Tanzania 2008 0 0 4 0 0 0 0 0
2009 4 0 0 0 0 0 0 0
Zimbabwe 1986 0 0 0 0 0 0 10 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 Ag3.10 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.