Patient p11

# samples
Time [days] RNA templates F1 F2 F3 F4 F5 F6
209 850 ok ok ok ok ok ok
332 1 000 ok ok ok ok ok ok
572 1 000 ok ok ok ok ok ok
1026 870 ok ok ok ok ok ok
1396 4 000 ok ok ok ok ok ok
1750 32 000 ok ok ok ok miss ok
2043 1 000 ok ok ok ok ok ok

Phylogenetic tree of V3 in patient p11.

  • RNA template counts are estimated two limiting dilutions series using fragment 4
  • An orange label for a fragment indicates problematic amplification and possible loss of variation.
  • A red label indicates a missing fragment.
Link color:
  • To display a phylogenetic tree of a particular region of the genome, select it in the pull-down menu.
  • Choices ending on minor include minor haplotypes from each time point, others display only consensus sequences
  • The size of the Tip circles indicate the frequency of the corresponding haplotype.
  • HIV recombines. Hence there trees don't necessarily depict the actual evolutionary history of the chosen part of the genome.
  • These are approximate maximum-likelihood trees generated with Fasttree

Note: low diversity might be due, in addition to biological reasons, to a low RT-PCR efficiency in a specific amplicon.

  • The top panels show divergence and diversity averaged in sliding windows of ??? bases for every position of the genome at particular time point.
  • The time point can be varied by moving the slider at the bottom.
  • The graph shows coverage at every postition in the genome.
  • The red line indicates the number of amplified RNA templates estimated from two limiting dilution series.
  • The each fragment corresponds to one of the peaks in coverage. Coverage tends to be lower towards the end of the fragments.
  • Where fragments overlap, the sum of reads from both fragments is reported
  • Some fragments amplify less well than other (F5 in particular). These tend to have low coverage or are sometimes missing completely.
  • The top panel shows single nucleotide polymorphism (SNP) frequencies through time. Color indicates position along the genome.
  • The panel below shows SNP frequencies at each position for a given time point. The color of each point equals that of the corresponding trajectory in the top panel.
  • The time point shown in the second panel can be chosen via the slider on top.
  • Clicking on an annotated element of the genome will zoom into that element.
Annotated genome sequence in genbank format:

Precompiled alignments

These alignments are premade for regions of general interest.

New alignments

Generate alignments for a custom genomic region.

From/To require HXB2 coordinates (both ends included).

NOTE: A few minutes might elapse while we prepare your data.

PBMC samples available for patient p11
Sample years on treatment good reads hypermutated
DNA 1 6.4 reads reads
DNA 2 8.4 reads reads
DNA 3 8.8 reads reads
  • Times indicate sampling times relative to start of treatment.
  • "Good" reads are those that map to p17gag and did not have obvious signs of hypermutation.
  • Hypermutated reads are those that map to p17gag and showed an excess of G-to-A mutations.

Tree of p17 before (RNA) and on treatment (DNA).