Table 4.

Summary statistics comparing each strain-specific assembly to the base assembly

	NL4-3		JR-CSF		HXB2		89.6		YU2
	Original	Strain specific	Original	Strain specific	Original	Strain specific	Original	Strain specific	Original	Strain specific
Total length	9166	9125	9166	9166	9166	9126	9166	9139	9166	9155
Aligned bases ref (%)	100	100	100	100	100	100	99.98	99.98	100	100
Aligned bases query (%)	100	100	100	100	100	100	99.98	99.98	100	100
Avg identity	96.04	97.17	97.39	99.19	95.81	96.70	93.82	96.41	94.81	95.69
Total SNPs	278	192	180	75	318	259	419	226	394	330
Total indels	83	58	11	1	81	55	72	9	56	33