RADSeq-derived SNP genotypes for 159 thornback ray Raja clavata from the Bay of Biscay
|Author(s)||Le Cam Sabrina1, Bidault Adeline2, Charrier Gregory2, Cornette Florence1, Lamy Jean-Baptiste1, Lapegue Sylvie1, Lorance Pascal1, Marandel Florianne1, Trenkel Verena1|
|Affiliation(s)||1 : Ifremer, France
2 : Brest university, France
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.
|Acknowledgments||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|