Table 1. jpHMM-assigned breakpoint locations (with 95% confidence intervals) for five HIV-1 A1/D recombinant sequencesa.
| Break point | Study number | Gene | Region | ||||
| 33365 | 8179 | 40534 | 11762 | 12792 | |||
| 1 | 1162 (1154–1170) | 1159 (1147–1171) | 1167 (1148–1186) | 1177 (1154–1200) | 1156 (1141–1171) | gag | p24 |
| 2 | 1843 (1809–1877) | 1844 (1809–1879) | 1844 (1809–1879) | 1958* (1811–2105) | 1828 (1809–1847) | gag | p24 |
| 3 | 2089 (2047–2131) | 2078 (2046–2110) | 2078 (2046–2110) | 2078 (2046–2110) | 2056 (2002–2110) | gag | p1 |
| 4 | 2489 (2463–2515) | 2489 (2465–2515) | 2489 (2465–2515) | 2487 (2475–2499) | 2598† (2463–2733) | pol | PR |
| 5 | 5981 (5951–6011) | 5979 (5953–6005) | 5976 (5951–6001) | 5985 (5973–5997) | 5998 (5989–6007) | tat/rev | |
| 6 | 6551 (6543–6559) | 6551 (6543–6559) | 6551 (6543–6559) | 6551 (6539–6563) | 6551 (6543–6559) | env | gp120 |
| 7 | 7247 (7234–7260) | 7246 (7231–7261) | 7249 (7232–7266) | 7483 (7471–7495) | 7214 (7171–7257) | env | gp120 |
| 8 | 8679 (8664–8694) | 8672 (8651–8693) | 8679 (8663–8695) | 8674 (8662–8686) | 8678 (8663–8693) | env | gp41 |
a Breakpoint locations as determined by jpHMM with HXB2 numbering. The breakpoint locations are generally consistent across the five specimens, indicating that the same A1/D recombinant structure is shared.
This corresponds to a region of subtype D uncertainty;
This corresponds to a region of subtype A uncertainty; refer to Figure 1. PR = Protease.