BergEtAl2017_AtlanticCod_TransatlanticDataset_PLINK-format

• Main Authors: Berg, Paul R., Star, Bastiaan, Pampoulie, Christophe, Bradbury, Ian R., Bentzen, Paul, Hutchings, Jeffrey A., Jentoft, Sissel, Jakobsen, Kjetill S.
• Format: Report
• Language: unknown
• Published: 2017
• Subjects: Chromosomal rearrangement; Ecological divergence; Genomic adaptation; Inversion polymorphism; Population genomics; SNPs; Arctic; Browns; Arctic cod; atlantic cod; Gadus morhua; Iceland; Northeast Arctic cod
• Online Access: http://hdl.handle.net/10255/dryad.154541; https://doi.org/10.5061/dryad.b20ps/1

SNP array data for 316 individuals of Atlantic cod (Gadus morhua), genotyped at 8,165 loci in standard PLINK file format. The PLINK file format consists of two files, a map file and a ped file. In the map file, the first column defines the linkage group, the second column contains the loci names (dbSNP accession numbers), the third line describes the position within the linkage groups (here all are set to 0) and the fourth column defines the order of the SNPs within each linkage group. In the ped file, column one is used to separate the populations (pop-1 to pop-9), column 2 defines the individuals within each population (denoted as the population abbreviation followed by the individual number) where the populations are abbreviated as follows: Can-N_PB = Placentia Bay, Can-N_SG = Southern Gulf of St. Lawrence, Can-S_SB = Sambro, Can-S_GM = Gulf of Maine, Can-S_BB = Browns Bank, Ice_F = Iceland Frontal, Ice_C = Iceland Coastal, NEAC = Northeast Arctic cod, NCC = Norwegian coastal cod. The genotypes are given as numbers from column 7 and onwards, where 1=A, 2=C, 3=G, 4=T. (For a thorough description of the PLINK format, please see https://www.cog-genomics.org/plink). All SNPs are referred to by their database of Single Nucleotide Polymorphisms (dbSNP) accession numbers, available from: http://www.ncbi.nlm.nih.gov/SNP.