Table 2. Measures of intra-host genetic diversity among DENV-1 lineages.

Genetic diversity was measured through SNPs analysis.

DENV-1 lineage	Name of the lineage	Strain	Total reads analysed	Mean Coverage/nt	Total nt variants a	Total number of variable sites		Est. mean genetic diversity (%) c
						n.t	a.a	n.t	a.a
Extinct	A	M32514	5919	454.20	130	10	0	0.023	n.a
	B	M31459	8330	736.47	51	0	0	n.a	n.a
		M36957	12127	1091.10	57	1	0	0.011	n.a
		M43826	3294	273.73	57	0	0	n.a	n.a
		M44988	15211	1334.72	59	0	0	n.a	n.a
Survived	C	M31987	17729	1621.37	5	0	0	n.a	n.a
		M47317 b	9333	824.04	56	0	0	n.a	n.a
		M47662	6300	561.02	4	1	0	0.009	n.a
		M49440	13439	1217.48	5	0	0	n.a	n.a
		M62690	3126	287.08	7	1	0	0.002	n.a
	D	M68417	8635	771.78	19	0	0	n.a	n.a
		M80579	1384	122.77	22	1	0	0.010	n.a
Control		I.C	6274	697.80	15	0	0	n.a	n.a

n.a; not applicable

^a The number of bases that are different from the reference genome.

^b Genetic diversity of recombinant DENV-1 strain showing in italic.

^c Estimated mean genetic diversity $=\frac{TotalVariants}{E\left(Depth\right)xLength}=\frac{{\sum }_{i=0}^n{FreqVariant}_{i}x{Depth}_i}{\frac{{\sum }_{i=0}^n{Depth}_i}{n}xLength}$ where n is the total number of variants.