TABLE 4.

Polymorphisms of IM-3 relative to the reference genome NC_007605.1

Sequence descriptiona	No. of bp considered	Polymorphism statistics			No. of SNPsb	Insertion and/or deletion (length [bp])
		No. of bp	%	No. of amino acids
Region between BNLF2a ORF and LMP1 ORF	673	26	3.86		26
oriP	1,355	30	2.21		20	Insertion (10 bp)
EBNA1 ORF	1,050	23	2.19	15	23
BHRF1 intron	439	8	1.82		8
Cp promoter (BCRF1 gene to W repeats)	1,719	31	1.80		29	Insertion (1 bp), deletion (1 bp)
EBNA2	1,272	20	1.57	11	17	Insertion (3 bp)
LMP2A exon 1	448	7	1.56	5	7
BRRF2 ORF	1,614	23	1.43	12	23
LMP1 ORF	842	11	1.31	9	11
RPSM1 promoter part between BART.I and BART.Ia	966	11	1.14		9	Insertion (1 bp), deletion (1 bp)
BDLF3 ORF	705	7	0.99	3	7
BBLF4 ORF	2,430	20	0.82	5	20
EBNA3C ORF + intron	2,746	22	0.80	11	22
BBLF2/BBLF3 ORF	2,130	14	0.66	4	11
BDLF2 ORF	1,263	8	0.63	4	8
BNRF1 ORF	3,957	25	0.63	9	25
BGLF3 ORF	999	6	0.60	1	6
BRLF1 ORF	1,818	10	0.55	4	10
Partial LMP2B gene (genome nt 1–1691)	1,691	9	0.53	1	9
BGLF1 ORF	1,521	7	0.46	2	4	Deletion (3 bp)
BPLF1 ORF	8,700	37	0.43	15	37
EBNA3A ORF	2,835	11	0.39	7	11
BBRF1 ORF	1,842	7	0.38	1	7
BOLF1 ORF	3,720	12	0.32	4	9	Insertion (3 bp)
BSLF1 ORF	2,625	4	0.15	1	6
Total (% of total)	49,360 (36.4)	389 (74.2)		124	365 (69.7)

^aSequences that had the largest numbers of polymorphisms. nt, nucleotide; ORF, open reading frame.

^bSNP, single-nucleotide polymorphism.