TABLE 1.
Covariation between codon 250 and other Gag sites in chronic subtype C sequencesa
| Codon 250 | Covarying codon | Association | TT | TF | FT | FF | Total | P | q-value |
|---|---|---|---|---|---|---|---|---|---|
| 250M | 252G | Negative | 55 | 317 | 34 | 7 | 413 | 7.4E–09 | 8.0E–06 |
| 260D | Positive | 264 | 108 | 4 | 37 | 413 | 1.9E–08 | 8.0E–06 | |
| 252S | Positive | 220 | 153 | 2 | 38 | 413 | 2.7E–07 | 7.0E–05 | |
| 247M | Negative | 0 | 372 | 4 | 36 | 412 | 2.5E–05 | 5.0E–03 | |
| 256V | Positive | 192 | 180 | 3 | 38 | 413 | 3.3E–05 | 5.0E–03 | |
| 207D | Positive | 38 | 334 | 0 | 41 | 413 | 2.2E–04 | 3.0E–02 | |
| 260E | Negative | 107 | 265 | 37 | 4 | 413 | 7.5E–04 | 8.0E–02 | |
| 250I | 252G | Positive | 33 | 6 | 55 | 318 | 412 | 1.4E–08 | 8.0E–06 |
| 260D | Negative | 4 | 36 | 264 | 110 | 414 | 1.4E–07 | 4.0E–05 | |
| 252S | Negative | 2 | 37 | 220 | 154 | 413 | 5.4E–07 | 1.0E–04 | |
| 256V | Negative | 3 | 37 | 192 | 181 | 413 | 5.0E–05 | 7.0E–03 | |
| 247 M | Positive | 4 | 35 | 0 | 374 | 413 | 5.9E–05 | 8.0E–03 | |
| 207D | Negative | 0 | 39 | 38 | 335 | 412 | 3.1E–04 | 3.0E–02 | |
| 260E | Positive | 36 | 4 | 109 | 265 | 414 | 8.2E–04 | 8.0E–02 |
a
TT, number of sequences with both codon 250 residueand covarying residue; TF, number of sequences with codon 250 residue butwithout covarying residue; FT, number of sequences without codon 250 residuebut with covarying residue; FF, number of sequences with neither codon 250residue nor covarying residue.