FIG 6.

Genomic variation in HIV-1. (A) Nucleotide diversity and genomic variation index (single-nucleotide polymorphisms relative to the genome) estimated using 100 accessions. Bars represent the averages and standard errors. (B) Genome-wide nucleotide variation. Single-nucleotide polymorphism (SNP) and nucleotide diversity (Pi) are plotted with respect to the genome. The average and 99% confidence interval (P < 0.01) are indicated as a horizontal line for each parameter. Coordinates are based on accession no. NC_001802.1. (C) Nucleotide diversity normalized to the length of the ORF or UTR.