Table 2.

Compartmentalization between blood and GT

	Full-length (HXB2 6600..7478)						Partitioned at GARD breakpoints
	Identical sequences present			Identical sequences removed
Donor ID	s	p(s’≤ s)*	q(s’ ≤ s)†	s	p(s’ ≤ s)	q(s’ ≤ s)	Region	s	p(s’ ≤ s)	q(s’ ≤ s)
RW36F	15	0.3902	0.2149	10	0.5976	0.2724	5′: 6600..7000	3	0.0225	0.0279
							3′: 7001..7478	7	0.4059	0.2205
RW56M	5	<0.0001	0.0004	4	<0.0001	0.0004	5′: 6600..6827	4	0.0298	0.0348
							Mid: 6828..7193	4	0.1932	0.1321
							3′: 7194..7478	3	0.0023	0.0057
ZM201F	20	0.0005	0.0018	16	0.0032	0.0067	5′: 6600..6879	13	0.0592	0.0471
							3′: 6880..7478	13	0.2361	0.1419
ZM216F	19	0.0073	0.0107	17	0.0535	0.0442	5′: 6600..6888	13	0.0507	0.0428
							3′: 6889..7478	15	0.0405	0.0376
ZM221F	7	<0.0001	0.0004	7	<0.0001	0.0004	5′: 6600..6898	5	<0.0001	0.0004
							3′: 6899..7478	6	0.0017	0.0045
ZM238F	11	<0.0001	0.0004	9	0.0036	0.0067	5′: 6600..6925	7	0.0274	0.0329
							3′: 6926..7478	7	0.4429	0.2374
ZM242M	2	<0.0001	0.0004	2	0.0376	0.0366	5′: 6600..6791	2	1.0000	0.4089
							Mid: 6792..7183	2	0.0004	0.0016
							3′: 7184..7478	2	1.0000	0.4089
ZM292F	13	<0.0001	0.0004	9	<0.0001	0.0004	5′: 6600..7186	10	0.0035	0.0067
							3′: 7187..7478	10	0.0713	0.0534

The SM test was performed on donor partners (Donor ID) using full-length envelope V1–V4 sequences (6600-7478, HXB2 nucleotide coordinates), full-length with identical sequences removed, and alignment regions (region) partitioned at genetic algorithm for recombination detection (GARD) breakpoints with identical sequences removed. The SM analysis used the observed number of migration events (s) to determine the P value (p).

*SM P value is the proportion of relabeled trees with as many or fewer migration events (s) as observed: p(s’ ≤ s), where s’ denotes results from 10,000 compartment-label permutations on the fixed tree, shown in bold, where P < 0.05.

^†Storey and Tibshirani (25) q value from SM P value, shown in bold, where q < 0.05.