104 cod from the National cod breeding program were selected for sequencing comprising 50 fish of NEAC origin, 11 fish of NCC origin and 43 fish offspring of NEAC x NCC crosses. The sequenced fish belonged to year classes 2005 (P) and 2006 (F1) and represented the second generation of cod produced in captivity. The original broodstock in the base population were sampled from different geographical areas along the Norwegian coast and were assigned to the NCC and NEAC populations based on sampling locations and the Pan IA and IB alleles (Fevolden & Pogson 1997 Bangera et al. 2011). Genomic DNA from the 104 breeding program fish was prepared for sequencing using the Truseq Library prep kit from Illumina (Illumina, San Diego, USA). Paired-end sequencing (2 x 100 nts) was carried out using an Illumina HiSeq 2000 instrument to generate approximately 10x coverage of the genome for each sample. Reads were processed using default parameters in Trimmomatic version 0.32 (Bolger et al. 2014) before being aligned to the unmasked reference genome based on the NCC map described above using Bowtie2 version 2.2.3 (Langmead & Salzberg 2012).