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Table 6 RAD-Seq SNPs located proximal to a putative gene

From: Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing

Parent No. of mapped SNPs No. of gene-associated SNPs (Stage 1) Percentage of gene-associated SNPs (Stage 1) No. of gene-associated SNPs (Stage 2) Percentage of gene-associated SNPs (Stage 2)
Br5 Mother 1,311 212 16.2 541 41.3
Br6 Mother 1,399 227 16.2 621 44.4
Br5 Father 1,833 327 17.8 843 46.0
Br6 Father 1,817 298 16.4 815 44.9
  1. The number of RAD-Seq SNPs located within or close to genes based on direct alignment of mapped RAD contigs (Stage 1; columns three and four) or Atlantic salmon reference genome contigs (Stage 2; columns five and six) against the stickleback nucleotide gene sequences downloaded from Ensembl BioMart (, Database = Ensembl Genes 72, Dataset = Gasterosterus aculeatus genes (BROADS1)). Column two gives the total number of sex specific segregating SNPs which were ordered and positioned within a linkage group using the Onemap software.