Table 2.

Annotation of each SNV and INDEL across the chIFITM1,2,3 genes

	aGenomic location	Reference/Variant 3′-5′ (5′-3′)	European	Commercial	Pirbright	Indigenous	Amino acid change (5′-3′)		Codon	Exon
IFITM1	SNVs
	13,141	G/A (C/T)	√	√	x	x	CGG to TGG	Arg to Trp	77	2
	14,105	C/T (G/A)	√	x	x	x	TCG to TCA	Ser to Ser	56	1
IFITM2	SNVs
	14,960	G/T (C/A)	√	√	√	√	CGG to AGG	Arg to Arg	111	2
	15,078	G/A (C/T)	x	x	x	√	GGC to GGT	Gly to Gly	72	2
	15,080	C/T (G/A)	x	√	x	√	GGC to AGC	Gly to Ser	72	2
	15,081	T/C (A/G)	√	√	√	√	GTA to GTG	Val to Val	71	2
	15,083	C/T (G/A)	x	√	x	x	GTA to ATA	Val to Ile	71	2
	15,084	G/A (C/T)	x	x	x	√	TTC to TTT	Phe to Phe	70	2
	16,175	A/C (T/G)	√	√	√	√	GCT to GCG	Ala to Ala	54	1
	16,193	G/A (C/T)	x	x	x	√	TTC to TTT	Phe to Phe	48	1
	16,242	T/C (A/G)	x	√	x	√	AAG to AGG	Lys to Arg	32	1
	16,292	G/A (C/T)	x	√	x	x	TAC to TAT	Tyr to Tyr	15	1
	16,295	G/A (C/T)	√	√	√	√	TCC to TCT	Ser to Ser	14	1
	16,303	T/C (A/G)	x	x	x	√	ATG to GTG	Met to Val	12	1
	INDELs
	16,243–16,244	TG/T (CA/A)	x	x	x	√	Frameshift		31	1
	16,269	A/ACC (T/GGT)	x	x	x	√	Frameshift		23	1
IFITM3	SNVs
	18,814	T/C (A/G)	√	x	x	x	ATG to GAG	Met to Glu	119	2
	18,862	C/T (G/A)	√	√	√	√	GTC to ATC	Val to Ile	103	2
	19,572	G/A (C/T)	x	x	x	√	TGC to TGA	Cys to STOP	59	1
	INDELs
	19,576–19,577	AC/A (GT/T)	x	x	x	√	Frameshift		58	1

^a These locations refer to the position on the PacBio consensus reference sequence already published and submitted [5]