Table 1. Candidate migration genes and protein products identified by both Stacks and Angsd. Chromosome number refers to Atlantic salmon genome.

Chromosome	SNP position	Distance to closest gene (bp)	Predicted protein	Gene symbol
2	13725458	48527 - 3′end	FXYD domain containing ion transport regulator 5a precursor	FXYD5A
2	19563669	2565 – 3′end	flotillin 1	FLOT1
2	24989435	0	progestin and adipoQ receptor family member 6-like isoform X2	PAQR6
2	27622691	1460 – 3′end	free fatty acid receptor 2-like	FFAR2
2	32550984	14430 – 5′end	plectin-like isoform X14	PLEC
9	48392079	16589 – 5′end	protocadherin gamma-A11-like	PCDHGA11
9	96081278	0	ATP-binding cassette sub-family F member 3-like	ABCF3
9	103885594	0	limbic system-associated membrane protein-like isoform X	LSAMP
9	103988881	0	limbic system-associated membrane protein-like isoform X	LSAMP