Supplemental Table S2 B.

Sequence	Genome contig	Gene name	Position	Ref	Var	Freq_AC	Freq_SB	FreqP_PL	FreqP_SB	FreqP_LB
NC_000861.1	n.a.	12S ribosomal RNA	1829	G	A	0 / 53	77 / 81	0 / 6	3 / 4	1 / 8
NC_000861.1	n.a.	16S ribosomal RNA	3119	A	T	46 / 87	18 / 28	0 / 8	0 / 8	0 / 8
NC_000861.1	n.a.	16S ribosomal RNA	3411	C	T	0 / 119	26 / 33	0 / 8	5 / 8	1 / 8
NC_000861.1	n.a.	tRNA-Lys	8876	C	A	73 / 779	74 / 352	0 / 4	0 / 4	n.a.
NC_000861.1	n.a.	NADH dehydrogenase 6	15240	G	A	2 / 3608	137 / 2702	2 / 4	0 / 4	n.a.
SS2U034121	AGKD01052493.1	Eukaryotic translation initiation factor 4 gamma 2	233	C	T	0 / 95	22 / 40	2 / 4	2 / 2	n.a.
SS2U054644	AGKD01031893.1	Uroporphyrinogen decarboxylase	1037	G	A	28 / 33	0 / 56	n.a.	n.a.	n.a.
SS2U054644	AGKD01031893.1	Uroporphyrinogen decarboxylase	1188	C	T	0 / 53	19 / 25	4 / 4	4 / 4	n.a.
SS2U054644	AGKD01031893.1	Uroporphyrinogen decarboxylase	1283	G	A	4 / 60	12 / 15	4 / 4	4 / 4	n.a.
SS2U055283	AGKD01013777.1	DNA2-like helicase	1822	G	A	1 / 65	25 / 50	3 / 4	n.a.	n.a.
SS2U055923	AGKD01022586.1	Bystin	615	G	A	106/109	7 / 190	0 / 4	n.a.	n.a.
SS2U058906	AGKD01005918.1	Mid1-interacting protein 1-like	350	G	T	0 / 49	67 / 68	4 / 4	4 / 4	n.a.

Sequence: name of the genebank sequence or EST-contig used as reference for mapped reads.

Genome contig: name of salmon genome (ICSASG_v1) contig with best sequence match to the respective EST-contig.

Ref: Reference variant.

Var: The derived variant.

Freq_AC and Freq_SB: Frequency of variant reads as fraction of total numbers of reads mapped in Aquaculture (AC) or Small benthic (SB).

FreqP: The frequency of variant in genotyping by PCR and direct sequencing, as a fraction of total number of chromosomes sequenced.