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#

Please note that, unless otherwise stated, all data on this release are subject to a publication embargo, described further in the Anopheles gambiae genomic surveillance project terms of use.

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-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-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
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
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.

Further reading#

We hope this page has provided a useful introduction to the Ag3.7 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.