TABLE 2.

Loci with variant allele frequencies between 25 and 75% at nucleotides 8500 to 150000 of NC_001664^a

Nucleotide no.	Virus strain	Sequencing depth	Variant frequency (%)	Polymorphism typeb	Gene	Change	Amino acid change	CDS codon no.	Protein effect
15942	HHV-6 CO4	22	31.80	SNP (transition)		C→T
15942	HHV-6 CO7	40	45.00	SNP (transition)		C→T
16978	HHV-6 CO4	35	40.00	SNP (transversion)	U7	G→T		38	None
16978	HHV-6 CO7	51	43.10	SNP (transversion)	U7	G→T		38	None
18687	HHV-6 CO4	37	48.60	SNP (transition)	U10	G→A	D→N	362	Substitution
18687	HHV-6 CO7	46	50.00	SNP (transition)	U10	G→A	D→N	362	Substitution
18877	HHV-6 CO4	33	48.50	SNP (transversion)	U10	C→A	P→H	425	Substitution
18877	HHV-6 CO7	32	59.40	SNP (transversion)	U10	C→A	P→H	425	Substitution
19258	HHV-6 CO7	30	50.00	SNP (transition)	U11	T→C	D→G	774	Substitution
19258	HHV-6 CO4	26	50.00	SNP (transition)	U11	T→C	D→G	774	Substitution
29716	HHV-6 CO7	19	36.80	SNP (transversion)	U19	T→A	K→I	368	Substitution
29716	HHV-6 CO4	15	53.30	SNP (transversion)	U19	T→A	K→I	368	Substitution
36965	HHV-6 CO7	47	34.00	Insertion (tandem repeat)	U26	(A)8→(A)9		282	Frame shift
36965	HHV-6 CO4	27	37.00	Insertion (tandem repeat)	U26	(A)8→(A)9		282	Frame shift
40589	HHV-6 CO4	42	31.00	SNP (transition)	U28	C→T		282	None
40589	HHV-6 CO7	42	50.00	SNP (transition)	U28	C→T		282	None
58704	HHV-6 CO4	21	33.30	SNP (transition)	U38	G→A		295	None
69117	HHV-6 CO4	33	45.50	SNP (transition)	U42	A→G		494	None
69117	HHV-6 CO7	58	50.00	SNP (transition)	U42	A→G		494	None
69133	HHV-6 CO7	60	48.30	SNP (transition)	U42	A→G	V→A	489	Substitution
69133	HHV-6 CO4	35	48.60	SNP (transition)	U42	A→G	V→A	489	Substitution
72012	HHV-6 CO7	49	51.00	SNP (transition)	U43	C→T	C→Y	465	Substitution
72012	HHV-6 CO4	39	56.40	SNP (transition)	U43	C→T	C→Y	465	Substitution
74768	HHV-6 CO4	42	66.70	SNP (transition)	U45	T→C	N→D	151	Substitution
74768	HHV-6 CO7	32	68.80	SNP (transition)	U45	T→C	N→D	151	Substitution
92258	HHV-6 CO7	45	33.30	SNP (transition)	U57	C→T	C→Y	552	Substitution
92258	HHV-6 CO4	30	36.70	SNP (transition)	U57	C→T	C→Y	552	Substitution
106203	HHV-6 CO4	21	33.30	SNP (transition)	U70	G→A		214	None
106203	HHV-6 CO7	45	48.90	SNP (transition)	U70	G→A		214	None
106566	HHV-6 CO4	32	37.50	SNP (transversion)	U70	T→A	D→E	335	Substitution
106566	HHV-6 CO7	39	59.00	SNP (transversion)	U70	T→A	D→E	335	Substitution
107612	HHV-6 CO4	28	57.10	SNP (transition)	U72	G→A	T→I	234	Substitution
107612	HHV-6 CO7	40	60.00	SNP (transition)	U72	G→A	T→I	234	Substitution
109716	HHV-6 CO7	37	43.20	SNP (transition)	U73	G→A		464	None
109716	HHV-6 CO4	40	55.00	SNP (transition)	U73	G→A		464	None
110489	HHV-6 CO4	33	42.40	SNP (transition)	U73	A→G	E→G	722	Substitution
110489	HHV-6 CO7	46	43.50	SNP (transition)	U73	A→G	E→G	722	Substitution
112286	HHV-6 CO7	44	40.90	SNP (transition)	U74	T→C	Y→H	551	Substitution
112286	HHV-6 CO4	42	61.90	SNP (transition)	U74	T→C	Y→H	551	Substitution
113466	HHV-6 CO4	25	60.00	SNP (transversion)	U76	G→T	H→N	598	Substitution
113466	HHV-6 CO7	46	65.20	SNP (transversion)	U76	G→T	H→N	598	Substitution
121571	HHV-6 CO4	11	63.60	Deletion	U79	-T		410	Frame Shift
121571	HHV-6 CO7	16	68.80	Deletion	U79	-T		410	Frame Shift
123584	HHV-6 CO4	22	36.40	SNP (transversion)	U83	A→T		19	None
123584	HHV-6 CO7	42	42.90	SNP (transversion)	U83	A→T		19	None
123591	HHV-6 CO4	20	30.00	SNP (transition)	U83	T→C	S→P	22	Substitution
123591	HHV-6 CO7	44	45.50	SNP (transition)	U83	T→C	S→P	22	Substitution

^aMatched loci with variant allele frequencies between 30 and 75%, coverage of >10× at nucleotides 8,500 to 150000 of NC_001664 for HHV-6A strains CO-4 and CO-7.

^bSNP, single nucleotide polymorphism.