TABLE 2.

Error rate distribution

Genomic regiona	Codonb	Sequencec	Error rate (mean ± SD)d
			Total	Point mutations	Indels
gag-pol	NAe	NA	0.0039 ± 0.0001	0.0017 ± 0.0001	0.0022 ± 0.0001
env-V3	NA	NA	0.0037 ± 0.0002	0.0012 ± 0.0001	0.0025 ± 0.0002
Protease	L10	cgacccCTCgtc	0.0353 ± 0.0086	0.0022 ± 0.0002	0.0331 ± 0.0051
	M46	accaaaaATGata	0.0920 ± 0.0056	0.0013 ± 0.0001	0.0907 ± 0.0043
	F53	aggtTTTatc	0.0436 ± 0.0034	0.0021 ± 0.0002	0.0415 ± 0.0022
RT	F77	agatTTCag	0.0205 ± 0.0028	0.0018 ± 0.0001	0.0187 ± 0.0011
	K101	gttaAAAcag	0.0295 ± 0.0044	0.0024 ± 0.0002	0.0271 ± 0.0032
	V179	ataGTCatc	0.0756 ± 0.0122	0.0036 ± 0.0002	0.0720 ± 0.0091
	G190	gtaGGAtct	0.0221 ± 0.0036	0.0012 ± 0.0001	0.0209 ± 0.0021
Integrase	G193	attgggGGGtac	0.1048 ± 0.0277	0.0089 ± 0.0003	0.0959 ± 0.0145
V3	R11	aagaaaaAGTatc	0.0256 ± 0.0037	0.0025 ± 0.0002	0.0231 ± 0.0020

^aHIV-1 genomic region analyzed. gag-pol and env-V3 correspond to the gag-p2/NCp7/p1/p6/pol-PR/RT/IN and V3 region of the gp120 in the envelope gene, respectively.

^bCodons associated with resistance to antiretroviral drugs were determined to have total error rate values of >1%.

^cNucleotide sequence based on the population sequencing of the HIV-1_NL4-3 clone (13), which around these codons was identical to the HIV-1_HXB2 reference sequence (GenBank accession no. K03455). The respective codons are indicated in uppercase letters, while the nucleotide positions associated with the elevated error rate (>1%) are shown in bold type. Position numbering is relative to the HIV-1_HXB2 reference sequence.

^dNumber of combined PCR and sequencing errors, i.e., point mutations, insertions, and deletions (indels), per read calculated using Segminator II (76). Mean and standard deviation values indicated were obtained from 10 independent sequences.

^eNA, not applicable.