Table 1.

SNPs detected by the variant-calling module in genes UL97 and UL54 for dataset Lon2_T3.

Gene	Position in genome	Position in protein	Frequency (%)	Nucleotide change	Codon change	Amino acid change
UL97	142,842	460	11.5	T → G	ATT → ATG	I → M
UL54	78,631	987	1.6	C → T	GCC → GTC	A → V
UL54	78,877	905	2.8	G → T	CGG → CTG	R → L
UL54	79,165	809	5.0	C → T	GCG → GTG	A → V
UL54	79,187	802	4.3	C → A	CTG → ATG	L → M
UL54	79,323	756	2.3	G → T	GAG → GAT	E → D
UL54	79,858	578	14.8	T → A	CTG → CAG	L → Q
UL54	80,052	513	4.2	T → G	AAT → AAG	N → K

Variants previously reported in this dataset (Houldcroft et al. 2016b) are shown in italic font.