Evolution of foot-and-mouth disease virus intra-sample sequence diversity during serial transmission in bovine hosts

Table 2 Consensus-level mutations, and their characterization

Position	Mutation	Frequency in sample	Gene	Syn/Nonsyn^a	Ts/Tv^b	Codon position	Sample^c
1087	C->T	54.4%	Leader	N: T->I	Ts	2	A2-2DPFC-PB
1164	A->G	63.9%	Leader	N: K->E	Ts	1	A2-6DPFC-PB
2417	C->A	51.1%	VP2	S: P->P	Tv	3	A2-6DPFC-PB
2417	C->A	52.8%	VP2	S: P->P	Tv	3	A3-3DPFC-PB
2754	C->T	> 60%	VP3	N: R->C	Ts	1	ALL BUT A1
2767	G->A	64.1%	VP3	N: G->D	Ts	2	A1-2DPFC-FLF
2768	C->T	52.8%	VP3	S: G->G	Ts	3	A3-3DPFC-PB
5435	C->T	> 55%	3A	S: G->G	Ts	3	ALL BUT A1 &
							A2-2DPFC-PB
							A2-3DPFC-SR
							A2-4DPFC-SR
							A2-5DPFC-SR
							A2-6DPFC-BRF
							A3-4DPFC-PB
5669	T->A	99.0%	3A	S: L->L	Ts	3	A2-6DPFC-FLF
5933	A->G	50.4%	3B2	S: K->K	Ts	3	A5-7DPFC-PB
6065	C->T	56.2%	3C	S: G->G	Ts	3	A3-1DPFC-PB
		99.7%					A3-3DPFC-SR
		99.3%					A3-4DPFC-SR
		75.6%					A3-5DPFC-PB
		99.6%					A3-5DPFC-SR
		99.7%					A3-5DPFC-BLF
		93.8%					A5-5DPFC-PB
		99.9%					A5-7DPFC-PB
6167	C->T	77.0%	3C	S: F->F	Ts	3	A2-6DPFC-FLF
7355	C->A	58.0%	3D	S: A->A	Tv	3	A2-2DPFC-PB
7376	T->C	54.4%	3D	S: D->D	Ts	3	A2-3DPFC-SR
		68.5%					A2-6DPFC-PB
		54.6%					A3-3DPFC-PB
7964	T->C	96.6%	3D	S: S->S	Ts	3	A3-3DPFC-SR
		97.6%					A3-4DPFC-SR
		53.4%					A3-5DPFC-PB
		99.1%					A3-5DPFC-SR
		99.9%					A3-5DPFC-BLF
		91.2%					A5-5DPFC-PB
		99.8%					A5-7DPFC-PB

^a Synonymous or Non-synonymous mutation with associated amino acid change.
^b Transition or Transversion.
^c Sample notation as described in the Material and Methods.
The mutation frequency is the weighted average frequency over the two sequencing runs for each sample.

ISSN: 1297-9716