Ag3.9
Contents
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 data@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:
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 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 Ag3.9 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.