Distinguishing HIV-1 drug resistance, accessory, and viral fitness mutations using conditional selection pressure analysis of treated versus untreated patient samples

Table 2 Significant differences of selection pressure between Treated and Untreated dataset

Position	Treated				Untreated				p-value
	K_a/K_s	N_a	N_s	LOD	K_a/K_s	N_a	N_s	LOD
10 ^a	1.47	516	176	5.4	0.21	172	401	71.57	< 0.0001
11	0.17	15	43	10.38	0.04	7	90	35.47	0.0017
17	0.06	17	142	49.46	0.16	55	176	40.54	0.0006
19	2.9	183	97	17.72	1.72	278	248	9.45	0.0004
20	0.39	137	131	12.56	0.07	41	215	80.54	< 0.0001
23	0.25	27	163	14.25	0.08	11	222	35.57	0.0006
24	1.59	85	64	2.49	0.33	22	79	6.73	< 0.0001
30	1.84	211	43	4.1	0.18	22	46	12.11	< 0.0001
32	0.53	49	46	3.08	0.01	2	69	31.72	< 0.0001
48	0.71	72	51	1.62	0.02	3	82	36.4	< 0.0001
50	0.9	27	13	0.51	0.07	2	12	5.74	0.0007
53	2.99	48	6	2.44	0.31	5	6	1.91	0.0032
54	1.55	246	69	3.25	0.03	7	112	50.03	< 0.0001
58	0.1	46	164	53.2	0.01	3	207	113.48	< 0.0001
61	0.1	55	211	70.15	0.05	63	431	172.9	0.0031
62	13.65	419	2	8.93	2.42	446	12	3.38	0.0094
63	6.1	1111	91	100.36	3.23	1343	208	71.62	< 0.0001
66	0.01	12	385	181.09	0.00	1	551	286.44	0.0002
67	0.2	64	118	26.07	0.10	75	290	95.99	0.0002
71	6.99	601	43	58.9	1.11	195	88	0.63	< 0.0001
73	1.81	130	36	3.17	0.05	5	48	18.6	< 0.0001
74	3.75	75	10	5.36	0.22	7	16	4.09	< 0.0001
76	1.02	34	40	0.28	0.16	10	74	11.25	< 0.0001
77	24.42	635	13	91.3	9.72	700	36	79.13	0.0025
82	4.58	339	37	25.9	0.46	51	56	4.77	< 0.0001
83	0.15	18	45	13.27	0.03	10	107	49.35	0.0006
84	1.46	112	5	0.56	0.00	0	14	300	< 0.0001
85	1.39	48	15	0.79	0.11	3	12	5.01	0.0001
88	0.82	154	70	1.11	0.1	25	95	32.49	< 0.0001
90	12.26	472	46	107.02	0.25	12	58	6.9	< 0.0001
92	0.1	34	131	44.36	0.04	25	211	90.47	0.0044

^a Mutations at codon in Italic are known associated with drug resistance. The nine codons that underwent a confident shift from positive selection in Treated to negative selection in Untreated are in bold.

ISSN: 1745-6150