Table 2.

Functional mutations (INDEL or SNVs) fixed in one of the rabbit lines and absent in the other line

OCUa	bpb	Lowc	Highd	Region	Gene	Mutationh
9	48,280,960	1/1	2/2	3ʹUTR	MC2R	3-bp deletioni
11	56,199,847	0/0e	1/1f	Frameshift	TTC23L	2-bp deletion
12	138,684,799	1/1	0/0	Frameshift	ENSOCUG00000031631	2-bp deletion
12	138,685,173	1/1	0/0	Frameshift	ENSOCUG00000031631	1-bp insertion
12	138,685,179	1/1	0/0	Frameshift	ENSOCUG00000031631	2-bp deletion
14	33,195,918	1/1	2/2g	3ʹUTR	ENSOCUG00000006264	25-bp deletioni
15	4,723,998	1/1	0/0	3ʹUTR	SLC18A1	4-bp deletion
19	40,686,575	0/0	1/1	5ʹUTR	FBXL20	90-bp insertion
19	43,006,505	0/0	1/1	Frameshift	GHDC	2-bp deletion
19	44,276,359	1/1	0/0	3ʹUTR	CD300LG	8-bp deletion

^aOryctolagus cuniculus (OCU) chromosome

^bFunctional mutation location in base pairs

^cGenotype of line with low V_E of LS

^dGenotype of line with high V_E of LS

^e0/0 indicates that the functional mutation is the homozygous for the reference allele

^f1/1 indicates that the functional mutation is homozygous for the alternative allele

^g2/2 indicates that the functional mutation is homozygous for a new allele not present in the reference genome

^hAll INDELs were marked according to the reference allele of OryCun v2.0.103

ⁱWith reference to the alternative allele of OryCun v2.0.103