How do I view a Sanger .ab1 or SCF trace (chromatogram) file?
In SnapGene 5.3 and later sequence traces can be viewed in "wrapped" mode
Open a Trace File
To open a trace file you can:
- Click menu File → Open File and browse to the location of the trace file, or
- Drag and drop a trace file into the SnapGene Launch window, or
- Double-click a trace file.
Change the Display Settings
In SnapGene 5.3 and later the default display will show the trace in "horizontal scrolling" (unwrapped) view. Use the horizontal scroll-bar to view the sequence.
Toggle the "Use Horizontal scrolling" button to show the sequence wrapped or unwrapped.
Use the vertical scroll-bar to view the sequence when in "wrapped" view.
Check the option to "Show quality values" to see a graph of quality values assigned to each nucleotide called by the DNA Sequencing Instrument.
Hover over any nucleotide call to see the "Peak Height" and "Quality" information associated with each peak. See this link for information about quality scores.
Use the x-axis and y-axis sliders to adjust the X and Y scale of the peaks.
Hover over any nucleotide call whilst holding the Option key (macOS) or ALT key (Windows and Linux) to see the raw peak values for each base at that position (Note that raw peak values are called by the sequencing instrument and stored in the .ab1 file, these values are not calculated by SnapGene).
Use the Arrows to view the trace in forward or flipped (reverse complement) orientation.
To learn how to edit trace files in SnapGene, see Edit a Sanger (.ab1, .scf or .ztr) Trace File.
View Advanced Information
By default SnapGene displays a trace as a Autoscaled trace so that peaks have a similar height across the length of the trace.
Click "Standard" to see the unscaled peaks. Click "Raw" to see raw peak data that has not been adjusted for differences in fragment mobility due to the presence of fluorophore-linked ddNTPs.
Click Chromatogram data to see information generated by the Sequencing Instrument.
View the "Sequence" tab to view the raw nucleotide calls generated by the sequencing instrument.
View the "Parameters" tab to see details of the instrument, software and settings used to generate the sequence trace.