Table 1.

Intra- and inter-isolate sequence comparison of entire haplotypes in Ug99 and Pgt21-0

	Sequence similarity		Structural variation
				Total variant size
Isolate comparison	Bases aligned (%)	Sequence divergence (%)	Number of variants	Mbp	% of genome
21-0A vs Ug99 A	99.64	0.08	491	0.82	0.46
Ug99 A vs Ug99 C	91.52	4.08	2571	13.69	7.88
21-0A vs Pgt21-0 B	91.38	4.19	2696	15.01	8.56
21-0 B vs Ug99 C	93.44	2.4	1910	11.50	6.69