Table 1 Genetic subtype, coreceptor usage, net charge and sequence coverage across V3 region in PBMC for the HIV-1 isolates
Sample ID | Subtype based on NFLG1 | geno2pheno (3.5 % FPR2) | Coverage including all short reads | Overall mean Div.% | Coverage of the V3 reads after filteration | Subtype based on the V3 sequence | Number of seq. with charges <5/≥5 |
|---|---|---|---|---|---|---|---|
10BR_001PE | B | ×4 | 322 | 1.1 | 132 | B | 06/126 |
10BR_003MG | BF1 | R5 | 9985 | 0.7 | 532 | F1 | 531/01 |
10BR_003SP | B | R5 | 876 | 1.4 | 296 | B | 270/26 |
10BR_007MG | B | R5 | 80 | 1.3 | 4 | B | 04/00 |
10BR_008SP | B | R5 | 655 | 0.7 | 120 | B | 119/1 |
10BR_009SP | B | R5 | 1031 | 1.0 | 290 | B | 271/19 |
10BR_010MG | BCF1 | R5 | 13756 | 1.0 | 763 | F1 | 736/27 |
10BR_010PE | B | R5 | 1103 | 0.8 | 345 | B | 330/15 |
10BR_011SP | CRF45_cpx | R5 | 24 | 0.8 | 10 | A1 | 10/00 |
10BR_014SP | B | R5 | 404 | 0.7 | 176 | B | 174/02 |
10BR_015RJ | BF1 | R5 | 3687 | 1.4 | 818 | F1 | 813/05 |
10BR_017SP | BF1 | R5 | 494 | 0.4 | 8 | F1 | 08/00 |
10BR_017MG | BF1 | R5 | 31 | 0.7 | 108 | F1 | 108/00 |
10BR_018PE | BC | R5 | 48 | 0.0 | 13 | B | 13/00 |
10BR_021SP | B | R5 | 838 | 1.0 | 289 | B | 288/01 |
10BR_023RJ | BF1 | R5/×4 | 446 | 1.5 | 248 | F1 | 248/00 |
10BR_026RJ | BF1 | R5 | 3281 | 1.1 | 888 | B | 48/840 |
10BR_029MG | B | ×4 | 282 | 0.0 | 1 | B | 00/01 |
10BR_029PE | BCF1 | ×4 | 909 | 0.9 | 183 | F1 | 06/177 |
10BR_032RJ | B | R5 | 1732 | 2.0 | 733 | B | 733/00 |
10BR_034MG | BF1 | R5 | 844 | 0.7 | 51 | B | 51/00 |
10BR_034PE | B | R5 | 679 | 0.9 | 369 | B | 350/19 |
10BR_035MG | B | R5 | 851 | 1.2 | 469 | B | 462/07 |
10BR_038SP | B | R5 | 2247 | 1.8 | 352 | B | 338/15 |
10BR_041RJ | BF1 | R5 | 342 | 0.8 | 160 | F1 | 147/13 |
10BR_042SP | B | R5 | 1269 | 2.0 | 293 | B | 279/14 |
10BR_043SP | B | ×4 | 65 | 1.7 | 26 | B | 006/2020 |
10BR_045SP | B | R5 | 137 | 0.0 | 8 | B | 08/00 |
10BR_046RJ | CRF70_BF1 | R5 | 112 | 0.4 | 32 | B | 32/00 |
10BR_046SP | CF1 | R5 | 2830 | 2.0 | 278 | C | 273/5 |
10BR_048SP | BF1 | R5 | 7 | 0.0 | 5 | B | 05/00 |
10BR_049SP | B | R5 | 632 | 3.5 | 44 | B | 44/0 |
10BR_050RJ | B | R5 | 1695 | 2.5 | 341 | B | 335/06 |
10BR_050SP | B | R5 | 1067 | 2.2 | 47 | B | 35/12 |
10BR_051RJ | B | ×4 | 4301 | 0.5 | 482 | B | 474/08 |
10BR_053PE | B | R5 | 2480 | 2.0 | 784 | B | 750/34 |
10BR_053RJ | BF1 | R5 | 3718 | 0.9 | 2011 | F1 | 1888/123 |
10BR_054RJ | B | R5 | 2173 | 0.9 | 745 | B | 655/90 |
10BR_055SP | B | R5 | 1393 | 1.5 | 59 | B | 59/00 |
10BR_056PE | B | R5 | 551 | 0.5 | 10 | B | 00/10 |
10BR_057SP | BF1 | R5 | 2704 | 0.6 | 1322 | F1 | 1319/3 |
10BR_091PE | B | R5 | 14026 | 0.8 | 2165 | B | 2161/4 |
10BR_097PE | B | R5 | 3773 | 3.3 | 697 | B | 675/22 |
10BR_098PE | B | R5 | 10215 | 5.3 | 1456 | B | 1311/145 |
10BR_100PE | B | R5 | 6060 | 3.7 | 614 | B | 613/01 |