Patient p4
Data summary of patient p4:
The different tabs below allow to browse- genetic diversity and divergence
- phylogenetic trees
- sequencing statistics
- dynamics of single nucleotide variants
- haplotypes
- subtype
- B
- # samples
- 8
| Time [days] | RNA templates | F1 | F2 | F3 | F4 | F5 | F6 |
|---|---|---|---|---|---|---|---|
| 78 | 450 | ok | ok | ok | ok | low | ok |
| 547 | 6 000 | ok | ok | ok | ok | ok | ok |
| 1127 | 2 000 | ok | ok | ok | ok | ok | ok |
| 1562 | 1 000 | ok | ok | ok | ok | ok | ok |
| 1948 | 940 | ok | ok | ok | ok | ok | ok |
| 2459 | 2 000 | ok | ok | ok | ok | low | ok |
| 2743 | 910 | ok | ok | ok | ok | ok | ok |
| 3054 | 1 000 | ok | ok | ok | ok | ok | ok |
Phylogenetic tree of V3 in patient p4.
Notes:
- 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.
Representation:
Link color:
Notes:
- 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.
Notes:
- 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.
Notes:
- 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.
Notes:
- 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: genome_p4.gb
Precompiled alignments
These alignments are premade for regions of general interest.
New alignments
Generate alignments for a custom genomic region.