Ag3.3#

The Ag3.3: Anopheles gambiae data resource contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 1002 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 Ag3.3.

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.

Please note, within this release, the study partner has waived the embargo for the following sample set:

  • 1178-VO-UG-LAWNICZAK-VMF00025 - 57 samples

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

Partner studies#

  • 1178-VO-UG-LAWNICZAK - Anopheles infectivity study (Uganda, Kenya)

  • 1190-VO-GH-AMENGA-ETEGO - Population genetics, parasite diversity and ecology of the major malaria vectors in the Kassena-Nankana Districts of Ghana

Whole-genome sequencing and variant calling#

All samples in Ag3.3 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 Ag3.3 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 Ag3.3 have been organised into 7 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
1178-VO-UG-LAWNICZAK 1178-VO-UG-LAWNICZAK-VMF00025 57
1190-VO-GH-AMENGA-ETEGO 1190-VO-GH-AMENGA-ETEGO-VMF00013 235
1190-VO-GH-AMENGA-ETEGO 1190-VO-GH-AMENGA-ETEGO-VMF00014 2
1190-VO-GH-AMENGA-ETEGO 1190-VO-GH-AMENGA-ETEGO-VMF00028 76
1190-VO-GH-AMENGA-ETEGO 1190-VO-GH-AMENGA-ETEGO-VMF00029 265
1190-VO-GH-AMENGA-ETEGO 1190-VO-GH-AMENGA-ETEGO-VMF00046 186
1190-VO-GH-AMENGA-ETEGO 1190-VO-GH-AMENGA-ETEGO-VMF00047 181

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 unassigned
study_id sample_set country year
1178-VO-UG-LAWNICZAK 1178-VO-UG-LAWNICZAK-VMF00025 Kenya 2017 1 0 0 0
Uganda 2013 0 0 1 0
2016 2 0 24 0
2017 1 0 28 0
1190-VO-GH-AMENGA-ETEGO 1190-VO-GH-AMENGA-ETEGO-VMF00013 Ghana 2016 4 204 26 1
1190-VO-GH-AMENGA-ETEGO-VMF00014 Ghana 2017 0 2 0 0
1190-VO-GH-AMENGA-ETEGO-VMF00028 Ghana 2017 1 74 1 0
1190-VO-GH-AMENGA-ETEGO-VMF00029 Ghana 2017 11 197 57 0
1190-VO-GH-AMENGA-ETEGO-VMF00046 Ghana 2017 7 163 16 0
1190-VO-GH-AMENGA-ETEGO-VMF00047 Ghana 2017 5 121 2 0
2018 4 49 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 Ag3.3 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.