Recommended File: tdf
Legacy Files: msf, pup, pileup
The pile up track can consists of to information parts. The first one, the coverage plot, is always present, the second, the SNP plot (Single-nucleotide polymorphism), is only displayed if the loaded data set has the required information.
Typically coverage-only data files are TDF files, while coverage+SNP files are prepared using samtools pileup. More information on preparing pile-ups
<bPile up track overview
Detailed description of component of the pile up track
You can also provide strand-specific TDF data:
A strand-specific coverage plots
The pile up track is used on two zoom levels.
Zoomed out enough, the view shows only the coverage plot and doesn't allow for hovering.
This coverage plot shows the number of matching reads with colors
| Color | Meaning |
|---|---|
| green | the number of matching reads on the forward strand |
| blue | the number of matching reads on the reverse strand |
| yellow | the sum of both. |
When zoomed in, an SNP track is added to the coverage plot, The SNP track shows mismatches per nucleotide. Also, Hovering over a position now shows you the exact number of matches, mismatches and coverage.
These colors are used According to the settings:
| Nucleotide | Color |
|---|---|
| A | Red |
| G | Blue |
| C | Yellow |
| T | Green |
