Ag3.8#

The Ag3.8: Anopheles gambiae data resource contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 2261 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 Ag3.8.

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 17th of November 2025.

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

Partner studies#

1230-VO-MULTI-AYALA - ANOSPP screening of Anopheles species and Plasmodium presence in malaria vectors in West-Central Africa (Gabon)
1288-VO-UG-DONNELLY - LLIN Evaluation in Uganda Project (LLINEUP)
1314-VO-BF-KIENTEGA - ANOSPP screening of Anopheles species and Plasmodium presence in malaria vectors in Burkina Faso
1315-VO-NG-OMITOLA - ANOSPP screening of Anopheles species and Plasmodium presence in malaria vectors in Nigeria
1326-VO-UG-KAYONDO - ANOSPP screening of Anopheles species and Plasmodium presence in malaria vectors in Uganda

This release also includes data from one study openly available in the literature: tennessen-2021.

Whole-genome sequencing and variant calling#

All samples in Ag3.8 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 Ag3.8 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 Ag3.8 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
1230-VO-MULTI-AYALA	1230-VO-MULTI-AYALA-AYDI-GA-2204	43
1288-VO-UG-DONNELLY	1288-VO-UG-DONNELLY-VMF00219	739
1314-VO-BF-KIENTEGA	1314-VO-BF-KIENTEGA-KIMA-BF-2104	179
1315-VO-NG-OMITOLA	1315-VO-NG-OMITOLA-OMOL-NG-2008	117
1326-VO-UG-KAYONDO	1326-VO-UG-KAYONDO-KAJO-UG-2203	975
tennessen-2021	tennessen-2021	208

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	unassigned
study_id	sample_set	country	year
1230-VO-MULTI-AYALA	1230-VO-MULTI-AYALA-AYDI-GA-2204	Gabon	2019	0	0	24	1	0	2
1230-VO-MULTI-AYALA	1230-VO-MULTI-AYALA-AYDI-GA-2204	Gabon	2020	0	0	15	0	0	1
1288-VO-UG-DONNELLY	1288-VO-UG-DONNELLY-VMF00219	Uganda	2017	17	0	0	323	0	0
			2018	59	0	0	70	0	1
			2019	26	0	0	243	0	0
1314-VO-BF-KIENTEGA	1314-VO-BF-KIENTEGA-KIMA-BF-2104	Burkina Faso	2017	7	19	0	15	0	0
			2018	9	16	0	18	0	0
			2019	36	43	0	16	0	0
1315-VO-NG-OMITOLA	1315-VO-NG-OMITOLA-OMOL-NG-2008	Nigeria	2018	0	16	0	101	0	0
1326-VO-UG-KAYONDO	1326-VO-UG-KAYONDO-KAJO-UG-2203	Uganda	2013	1	0	0	46	0	0
			2014	0	0	0	153	0	0
			2015	2	0	0	94	0	0
			2016	0	0	0	131	0	0
			2017	19	0	0	190	0	0
			2018	12	0	0	327	0	0
tennessen-2021	tennessen-2021	Burkina Faso	2011	0	18	0	0	41	0
			2012	0	63	0	0	0	0
			2015	0	33	0	0	0	0
			2016	0	53	0	0	0	0

Note that there can be multiple sampling sites represented within the same sample set.

MalariaGEN vector data user guide

Ag3.8

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