Viral load is a routine test that measures the concentration HIV-1 RNA in the patient's blood.
CD4+ counts measures the concentration of CD4+ immune cells, that are a standard indicator for disease progression. The lower the CD4+ counts, the more advanced the stage of the infection.
The HIV-1 genome from each patient is annotated with genes, proteins, RNA structures, and other features of interest.
From each HIV-1 sample, the consensus sequence represent approximately the major variant.
Phylogenetic trees are a representation of the genetic distances between HIV-1 sequences.
Trees for both major and minor genetic variants are provided.
Within an infection, divergence measures the average genetic distance an HIV-1 from the founder strain.
Diversity measures the average distance between sequences within the same sample.
Local divergence and diversity measure genetic distances in small windows along the genome.
Coverage quantifies how many sequencing reads covering a certain genomic site have been obtained.
Single nucleotide variants appear during the infection at many genomic sites. Their frequency within the HIV-1 population is tracked in time.
Haplotypes are genetic variants over whole genomic regions, including correlations between sites.
The data includes haplotype information on regions as long as 500 bp.
Both premade alignments and custom regions can be queried.