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

BMC Genomics

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

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

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 (http://www.ensembl.org/biomart/martview/, 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.

ISSN: 1471-2164