Table 2. Estimated frequencies of reconstructed haplotypes over the full-length coding region.
| Estimated frequencies% (mean ± sd)a | |||||
|---|---|---|---|---|---|
| NGS platform | HIV-1 89.6 | HIV-1 HXB2 | HIV-1 JR-CSF | HIV-1 NL4–3 | HIV-1 YU2 |
| 454/Roche | 14.4 ± 0.4 | 11.0 ± 0.4 | 19.9 ± 0.5 | 43.5 ± 1.0 | 11.1 ± 0.4 |
| Illumina | 22.6 ± 0.3 | 10.0 ± 0.4 | 29.6 ± 0.4 | 26.9 ± 0.4 | 10.9 ± 0.3 |
| PacBio | 17.6 ± 0.3 | 5.9 ± 0.5 | 27.1 ± 0.5 | 36.2 ± 0.5 | 13.1 ± 0.4 |
NGS, next-generation sequencing.
aFor each platform, we computed mean and standard deviation of full-length reconstructed haplotype frequencies of 100 bootstrap samples from 179 521; 1 365 693 and 10 651 reads for 454/Roche, Illumina and PacBio, respectively.