RADSeq-derived SNP genotypes for 159 thornback ray Raja clavata from the Bay of Biscay

Date 2019-12-06
Author(s) Le Cam SabrinaORCID1, Bidault Adeline2, Charrier GregoryORCID2, Cornette Florence1, Lamy Jean-BaptisteORCID1, Lapegue SylvieORCID1, Lorance PascalORCID1, Marandel FlorianneORCID1, Trenkel VerenaORCID1
Affiliation(s) 1 : Ifremer, France
2 : Brest university, France
DOI 10.17882/70648
Publisher SEANOE

We developed a panel of single nucleotide polymorphism (SNP) markers for 159 thornback ray Raja clavata sampled in the Bay of Biscay during the period 2011-2016 using a RADSeq protocol. Demultiplexed sequences were aligned to the genome of Leucoraja erinacea which was used as reference genome. From an initial set of 389 483 putative SNPs, we only retained loci with a calling frequency percentage above 50%, MAF (minor allele frequency) above 0.01 and read depth below 500 to remove spurious SNPs. This resulted in selecting 43 088 SNPs. The genotype data is provided in variant call format (vcf ). Note that contigs contain several SNPs.

Licence CC-BY-NC-SA
Acknowledgements The creation of this SNP data set was funded by the French “Agence Nationale de la Recherche” (ANR) under the GenoPopTaille project (ANR-14-CE02-0006-01) and by the European Union's Horizon 2020 research and innovation programme under the grant agreement No. 773713
File Size Format Processing Access
vcf file (see DataDescription.txt) 8 MB TEXTE Processed data Open access
Inofration on samples (see DataDescription.txt 7 KB CSV Raw data Open access
Data description 1 KB TEXTE Open access
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How to cite 

Le Cam Sabrina, Bidault Adeline, Charrier Gregory, Cornette Florence, Lamy Jean-Baptiste, Lapegue Sylvie, Lorance Pascal, Marandel Florianne, Trenkel Verena (2019). RADSeq-derived SNP genotypes for 159 thornback ray Raja clavata from the Bay of Biscay. SEANOE. https://doi.org/10.17882/70648