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Table 1 Genetic subtype, coreceptor usage, net charge and sequence coverage across V3 region in PBMC for the HIV-1 isolates

From: Frequency of coreceptor tropism in PBMC samples from HIV-1 recently infected blood donors by massively parallel sequencing: the REDS II study

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
  1. 1Near Full-Length genomes, 2 False positive rate