Table 2. Genetic variation annotation of DA and F344.

	SNPsa			Indels			Structural variant
	DA	F344	Shared	DA	F344	Shared	DA	F344
Intergenic region	658,646	660,019	1,150,467	85,753	91,326	97,035	—	—
Intron	485,087	489,738	837,376	70,958	73,231	75,716	17516	19607
Downstream (up to 5 kb)	71,596	71,646	123,030	10,565	10,620	10,722	—	—
Upstream (up to 5 kb)	70,831	71,107	119,219	10,109	10,413	9,853	—	—
3′ UTR	4,094	3,766	6,955	685	723	811	291	305
5′ UTR	752	647	1,061	48	37	47	226	239
Start gained in 5′ UTR	128	122	157	—	—	—	—	—
Coding sequences and splice sites							2572	2829
Synonymous coding	7,146	6,981	12,104	—	—	—	—	—
Nonsynonymous coding	4,230	4,060	7,187	—	—	—	—	—
Frameshift	—	—	—	156	135	217	—	—
Start lost	1	6	8	—	—	—	—	—
Stop gained	35	35	59	—	—	—	—	—
Stop lost	4	1	6	—	—	—	—	—
Splice-site acceptor	30	31	59	35	21	58	—	—
Splice-site donor	26	27	58	32	16	62	—	—
Synonymous stop	3	5	10	—	—	—	—	—
Nonsynonymous start	1	0	2	—	—	—	—	—
Codon deletion	—	—	—	19	10	14	—	—
Codon change + codon deletion	—	—	—	10	2	6	—	—
Codon insertion	—	—	—	12	4	5	—	—
Codon change plus codon insertion	—	—	—	7	4	4	—	—
Within noncoding gene
Nonsynonymous coding	434	428	866	—	—	—	—	—
Synonymous coding	232	228	395	—	—	—	—	—
Stop gained	24	14	27	—	—	—	—	—
Stop lost	6	15	18	—	—	—	—	—
Synonymous stop	3	0	6	—	—	—	—	—
Start lost	3	1	1	—	—	—	—	—
Synonymous start	1	0	0	—	—	—	—	—
Codon change + codon deletion	—	—	—	3	0	2	—	—
Codon deletion	—	—	—	2	1	2	—	—
Codon insertion	—	—	—	1	0	2	—	—
Codon change + codon insertion	—	—	—	0	1	0	—	—

Calculated using SNPEff v.1.9.5 (Cingolani et al. 2012) and Ensembl’s R. norvegicus build 3.4.64.

^aHomozygous SNPs.