. 2016 Nov 1;32(10-11):1031–1045. doi: 10.1089/aid.2015.0330

Table 5.

Residues in Vpr That Differed in Frequency of the Dominant Amino Acid

Codon	Infection stage	Residue frequency	Signature residue	p	q
19	Chronic	A_0.27, I_0.01, T_0.72	A	.180	0.70
	t/f	T_0.88, A_0.12
22	Chronic	L_0.49, I_0.45, V_0.05, M_0.01	L	.007	0.14
	t/f	L_0.82, I_0.18
41	Chronic	S_0.5, G_0.24, N_0.2 D_0.04, A_0.01, H_0.01, I_0.01	S	.332	0.80
	t/f	S_0.65, G_0.35
55	Chronic	T_0.79, A_0.13, M_0.04, L_0.01, P_0.01, R_0.01, S_0.01, I_0.01	T	.143	0.70
	t/f	T_0.65, A_0.12, V_0.12, E_0.06, I_0.06
60	Chronic	I_0.58, L_0.39, M_0.02, V_0.01	I	.147	0.70
	t/f	I_0.76, L_0.18, M_0.06
61	Chronic	I_0.83, L_0.08, M_0.03, T_0.05, V_0.01	I	.193	0.70
	t/f	I_0.71, L_0.18, T_0.06, V_0.06
70	Chronic	I_0.82, V_0.11, T_0.06, M_0.01	I	.023	0.28
	t/f	I_0.59, V_0.29, T_0.12
84	Chronic	L_0.63, I_0.11, M_0.11, V_0.07, W_0.04, T_0.02, G_0.01, S_0.01	L	.209	0.70
	t/f	L_0.47, I_0.12, M_0.12, V_0.12, A_0.06, S_0.06, T_0.06
93	Chronic	A_0.9, S_0.06, T_0.03, D_0.01, P_0.01	A	.005	0.14
	t/f	A_0.65, S_0.18, P_0.12, N_0.06

The bold values highlight residues that can more likely be explored as possible transmission signatures that have a p-value < 0.05 and a q-value threshold < 0.3 to correct for multiple hypothesis testing, for which we used the Benjamini-Hochberg procedure to compute false discovery rate-adjusted p-values (q-values).