Ag3.5#

The Ag3.5: Anopheles gambiae data resource contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 1140 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 Ag3.5.

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#

  • 1264-VO-CD-WATSENGA - PAMCA Anopheles genomics programme - First investigation of genetic diversity in malaria vectors in the Democratic Republic of Congo and the implications for the spread of insecticide resistance

  • 1270-VO-MULTI-PAMGEN - Pan-African Malaria Genetic Epidemiology Network (PAMGEN) Anopheles gambiae samples

  • 1272-VO-GM-OPONDO - PAMCA Anopheles genomics programme - Understanding genomic diversity and heterogeneity of insecticide resistance phenotypes in Anopheles gambiae s.l. in The Gambia

Whole-genome sequencing and variant calling#

All samples in Ag3.5 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 Ag3.5 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 Ag3.5 have been organised into 4 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
1264-VO-CD-WATSENGA 1264-VO-CD-WATSENGA-VMF00161 508
1264-VO-CD-WATSENGA 1264-VO-CD-WATSENGA-VMF00164 165
1270-VO-MULTI-PAMGEN 1270-VO-MULTI-PAMGEN-VMF00162 85
1272-VO-GM-OPONDO 1272-VO-GM-OPONDO-VMF00160 382

Here is a more detailed breakdown of the samples contained within this sample set, summarised by country, year of collection, and species:

taxon arabiensis gambiae gcx1 gcx2 unassigned
study_id sample_set country year
1264-VO-CD-WATSENGA 1264-VO-CD-WATSENGA-VMF00161 Democratic Republic of the Congo 2013 0 77 0 0 0
2014 0 54 0 0 0
2016 0 157 0 0 0
2017 0 160 0 0 0
2018 0 60 0 0 0
1264-VO-CD-WATSENGA-VMF00164 Democratic Republic of the Congo 2019 0 20 0 0 0
2020 0 145 0 0 0
1270-VO-MULTI-PAMGEN 1270-VO-MULTI-PAMGEN-VMF00162 Ethiopia 2020 85 0 0 0 0
1272-VO-GM-OPONDO 1272-VO-GM-OPONDO-VMF00160 Gambia, The 2001 1 0 0 0 0
2019 313 19 6 37 6

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 Ag3.5 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.