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Amin1 SNP data release

Released on 12 Nov 2021.

Mosquito

This data release includes whole genome sequences from 302 wild-caught mosquitoes collected from five sites in Cambodia. The mosquitoes included in this study were An. minimus s.s.. All mosquitoes were sequenced using Illumina technology with 150bp long reads by the Wellcome Sanger Institute Parasite and Microbes Programme.

Data sets

Data availability

This data release includes sample metadata, whole genome sequence data, and genome-wide SNP calls from whole genome sequencing of 302 wild-caught mosquitoes collected from Cambodia. These individuals are all An. minimus s.s. These data are hosted in Google Cloud. For more information about downloading data, please see the data download guide. For more information about accessing data in the cloud, please see the cloud data access guide.

Contributing studies

Mosquito specimens sequenced for this data release come from three separate field studies in Cambodia, led by Dr. Brandy St. Laurent in collaboration with the National Center for Parasitology, Entomology, and Malaria Control (CNM) Cambodia and the NIH NIAID Laboratory of Malaria and Vector Research. These collections were done in 2010 in Thmar Da, in Eastern Cambodia, a longitudinal collection over 2014 in two sites in each of Pursat, Preah Vihear, and Ratanakiri provinces, and quarterly collections over 2016 in one site each in Pursat and Preah Vihear province, Cambodia. Multiple Anopheles species were collected in each of these studies, including the An. minimus s.s. specimens that have been included in this study. Field specimens were stored in 1.5 ml tubes with silica gel dessicant. DNA was extracted using either Nextec plates or a CTAB DNA extraction method. GPS coordinates for collections are available in the sample metadata.

Whole genome sequencing and variant calling

The methods for sequencing and variant calling closely follow Ag1000G. 150bp sequence reads were aligned to the An. minimus reference genome AminM1.

Open access

Our approach to sharing data

Data package contact

Citations

Please acknowledge and cite the source of the data using the following format: “This publication uses data from the MalariaGEN Vector Observatory – Asia as described in ‘Population genomics reveal distinct and diverging populations of An. minimus in Cambodia – a widespread malaria vector in Southeast Asia; Brandyce St. Laurent et al; bioRxiv 2021.11.11.468219; doi: https://doi.org/10.1101/2021.11.11.468219‘”