Origin of samples and genome sequence coverage

Genomic DNA was extracted from fin clips of 61 rainbow trout. Whole-genome paired-end sequencing libraries were prepared and sequenced using the Illumina HiSeq 2000 or 2500 platforms providing an average of 15X and minimum of 8X genome coverage per sample. The sequenced samples included 11 clonal lines from WSU (Table ​(Table1),1), 38 steelhead and resident rainbow trout from wild and hatchery-origin populations distributed throughout the native range of the species, and 12 fish from the AquaGen rainbow trout aquaculture breeding program. The population of origin and genome sequence coverage of each sample are given in Supplemental File S1.

List of the 11 clonal doubled haploid rainbow trout and steelhead lines used in this whole-genome resequencing for SNP discovery study.

Information is also provided on the Swanson line, which is the source of the current rainbow trout reference genome.