Table 2.

Twenty-five highest correlated pairs of amino acid residues in the protease gene of HIV found by CoVaMa in an RNAseq study of a large cohort of drug-resistant HIV patients.

Pair 1	Pair 2	LD	References of known associations
41K-93L	41R-93I	0.063462	[7, 30]
77I-93L	77V-93I	0.056952	[27–30]
46L-82A	46M-82V	0.056426	[7, 27, 28]
30D-88N	30N-88D	0.055541	[7, 27, 28]
10I-93L	10L-93I	0.052307	[7, 27–29]
35D-36I	35E-36M	0.051156	[7, 27–29]
63L-93I	63P-93L	0.051149	[30]
10I-62V	10L-62I	0.050766	[27]
63L-90L	63P-90M	0.04806	[27, 28]
10I-90M	10L-90L	0.047771	[27, 28]
36I-77V	36M-77I	0.042961	[27, 29, 30]
62I-71A	62V-71V	0.040321	[29]
46I-90M	46M-90L	0.040264
41K-63P	41R-63L	0.03999
54I-82V	54V-82A	0.039912	[27]
62I-93I	62V-93L	0.039224	[27, 30]
10I-82A	10L-82V	0.037066	[27, 28]
10I-35D	10L-35E	0.036709
36I-62V	36M-62I	0.036042	[27–29]
10I-36I	10L-36M	0.034866
62I-63L	62V-63P	0.034603	[30]
30D-35E	30N-35D	0.034588	[7]
71A-93I	71V-93L	0.034398	[29, 30]
10I-71V	10L-71A	0.034022	[27–29]
62I-90L	62V-90M	0.033936	[27]