Table 2 Evaluation of the compartmentalization between pairs of samples from the same patient with Wright’s measure (Fst). The p-value was calculated by randomly assigning the sequences to the compartments and re-calculate the Fst. 100 resampling were performed in each pair of comparisons.

From: Characterization of HIV-1 diversity in various compartments at the time of primary infection by ultradeep sequencing

Patient Pairs of compartments		Fst all reads		Fst one sequence by Cluster		Slatkin-madisson
Patient Pairs of compartments		Fst estimated	P-value	Fst estimated	P-value	% of significant permutations	Comparmentalization
PHI2	WB-PL	0.018	0.314	0.001	0.412	13	No
PHI2	WB-SF	0.014	0.275	−0.001	0.667	38	No
PHI2	PL-SF	0.069	0.010	0.001	0.245	29	No
PHI3	WB-PL	−0.009	0.637	−0.046	0.931	1	No
PHI3	WB-SF	0.012	0.363	0.004	0.451	2	No
PHI3	PL-SF	−0.007	0.559	−0.021	0.618	1	No
PHI4	WB-NSC	0.693	<0.0001*	0.316	<0.0001*	100	Yes
PHI4	WB-PL	0.028	0.216	0.010	0.069	44	No
PHI4	PL-NSC	0.690	<0.0001*	0.304	<0.0001*	100	Yes
PHI4	WB-SF	0.223	<0.0001*	0.046	<0.0001*	58	No
PHI4	NSC-SF	0.692	<0.0001*	0.286	<0.0001*	100	Yes
PHI4	PL-SF	0.690	<0.0001*	0.018	<0.0001*	16	No
PHI5	PL-WB	0.273	<0.0001*	0.157	<0.0001*	100	Yes
PHI5	WB-SF	0.412	<0.0001*	0.196	<0.0001*	100	Yes
PHI5	PL-SF	0.892	<0.0001*	0.752	<0.0001*	100	Yes
PHI5	PL-SAL	0.653	<0.0001*	0.556	<0.0001*	100	Yes
PHI5	WB-SAL	0.119	<0.0001*	0.157	<0.0001*	100	Yes
PHI5	SF-SAL	0.735	<0.0001*	0.495	<0.0001*	100	Yes
PHI6	WB-NSC	0.029	0.225	0.073	0.382	8	No
PHI6	WB-PL	0.167	0.059	0.009	0.402	6	No
PHI6	NSC-PL	−0.260	0.853	−0.120	0.706	2	No
PHI6	WB-SF	0.390	0.049	0.117	0.098	11	No
PHI6	NSC-SF	0.145	0.147	−0.031	0.559	16	No
PHI6	PL-SF	−0.157	0.941	−0.064	0.657	13	No
PHI6	WB-SAL	−0.115	0.902	−0.066	0.931	4	No
PHI6	NSC-SAL	−0.234	0.902	−0.362	0.863	3	No
PHI6	PL-SAL	0.227	0.020	−0.066	0.922	8	No
PHI6	SF-SAL	0.169	0.137	−0.286	0.941	14	No
PHI7	PL-WB	0.208	<0.0001*	0.111	<0.0001*	100	Yes
PHI7	WB-SF	−0.002	0.529	−0.010	0.824	100	No
PHI7	PL-SF	0.284	<0.0001*	0.135	<0.0001*	100	Yes
PHI8	PL-SF	−0.041	0.873	−0.032	0.941	75	No
PHI8	PL-SAL	−0.019	0.725	−0.020	0.951	59	No
PHI8	SF-SAL	0.022	0.284	−0.002	0.716	44	No

*Significant p-values, SF: seminal fluid, WB: Whole blood, PL: Plasma, SAL: saliva, NSC: non spermatozoid cells.

Back to article page

Table 2 Evaluation of the compartmentalization between pairs of samples from the same patient with Wright’s measure (Fst). The p-value was calculated by randomly assigning the sequences to the compartments and re-calculate the Fst. 100 resampling were performed in each pair of comparisons.

Search

Quick links