Table 1.

Details of linkage disequilibrium

	Sites	LD #1	LD #2	LD #1 Codon = Amino	LD #2 Codon = Amino	Gene
	1627	T	C	CT[T] = L	CT[C] = L	nsp2
	9866	C	T	[C]TT = L	[T]TT = F	nsp4
	12 160	A	G	GA[A] = E	GA[G] = E	nsp8
LD Set 1				IHVdel	A[TA] = I [CAT] = H [G]TC = V
	21 765–21 770	–	tacatg			S
	22 917	G	t	C[G]G = R	C[T]G = L	S
	23 018	G	t	[G]TT = V	[T]TT = F	S
	23 040	A	G	C[A]A = Q	C[G]A = R	S
	26 529	A	G	[A]AT = N	[G]AT = D	M
	26 858	C	T	TT[C] = F	TT[T] = F	M
	27 259	A	C	[A]GG = R	[C]GG = R	ORF6
	27 382–27 384	GAT	CTC	GAT = D	CTC = L	ORF6
	27 889	T	C	–	–	–
	28 330	G	A	GG[G] = G	GG[A] = G	N
	12 310	A	G	CA[A] = Q	CA[G] = Q	nsp8
LD Set 2	16 616	A	C	A[A]T = N	A[C]T = T	nsp13
	27 012	T	C	[T]TG = L	[C]TG = L	M
	27 513	T	C	TA[T] = Y	TA[C] = Y	ORF7a
LD Set3	19 677	T	G	CA[T] = H	CA[G] = Q	nsp15
	21 306	T	C	CG[T] = R	CG[C] = R	nsp16
	22 812	C	A	A[C]G = T	A[A]G = K	S
LD Set 4	8991	T	C	G[T]A = V	G[C]A = A	nsp4
	25 810	T	C	[T]TT = F	[C]TT = L	ORF3a

Note: The genomes will either have LD Pattern 1 or LD Pattern 2 across the positions in each LD set.