Table 4.

POL gene subtype composition identified by jpHMM in recombinants (% of gene that is subtype B).

	Gene
Sample	Protease∗	RT†	Rnase H‡	Integrase§
10.ph17	AE	AE/B (87.6%)1	B	B
13.ph17	AE	AE	AE	B (96%)
20.ph17	AE	AE	AE	B (95.7%)
21.ph17	B	B (∼86.7%)/AE	AE	AE
35.ph17	AE/B (∼57.5%)	B (∼36.4%)/AE	AE	AE
36.ph17	AE/B (∼53.5%)	B (38.2%)/AE	AE	AE
7.ph18	AE	AE	AE	AE/B (32.5%)/AE2
17.ph18	AE	AE/B (87.6%)3	B	B
32.ph18 4	AE	AE	AE/B (86.9%)	B (53.9%)/AE
27.ph17	AE	AE	AE/B (97.2%)	B (55.8%)/A1
34.ph17	A1	A1	A1	A1
31.ph18	G	G/A1 (48.6%5	A1 (80.6%)/G	G

^∗jpHMM POL location (HXB2 numbering) 2253–2550

^†jpHMM POL location (HXB2 numbering) 2550–3870

^‡jpHMM POL location (HXB2 numbering) 3870–4230

^§jpHMM POL location (HXB2 numbering) 4230–5096

¹subtype designation from 5’end - 3’end of gene; % calculated from breakpoints identified by jHMM

²breakpoints for subtype B portion in the the middle of the gene flanked by AE portions

³Stanford and Rega analysis classified p-RT together as B/A1

⁴breakpoints for subtype B portion in the middle of Rnase H and Integrase

⁵percentage of subtype in recombinants that do not have subytpe B.