How do I view a Sanger trace (chromatogram) file?
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 side panel, or
- Double-click a trace file (.ab1, .scf or .ztr formats).
Change the Display Settings
The default view will show the trace in "Linear" (unwrapped) view. Use the horizontal scroll-bar to view the sequence.
Click the "Wrap to Window" button to show the sequence in a "wrapped" view.
Use the vertical scroll-bar to view the sequence.
Click Display → Use Full Height if you want to fit the trace to the full height of the window in "Linear" view.
Change SnapGene Preferences if you want to show the base calls below the peaks. See Set Display Options for Chromatograms for details. Note this preference will change the view for all trace files.
Toggle the "Show quality values" button to see bars representing quality values assigned to each nucleotide by the DNA Sequencing Instrument.
Hover over any position to see the raw"Peak Height" and "Quality" information associated with the major peak. See this link for information about quality scores.
Hover over any nucleotide call whilst holding the option key (macOS) or ALT key (Windows and Linux) to see the raw peak height values for each base at that position.
Alternatively, show the quality values and hover over the quality bars to see the raw peak values.
Raw peak values are called by the sequencing instrument and stored in the .ab1 file, these values are not calculated by SnapGene
Use the Arrow buttons to view the trace in forward or flipped (reverse complement) orientation.
To learn how to edit trace files in SnapGene, see Edit a Sanger 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.
Switch to "Parameters" view to see metadata saved with the file by the Sequencing instrument that created the sequence trace.
Changes SnapGene Preferences if you want to see a View for "Raw" peaks with uncorrected mobility. See Set Display Options for Chromatograms for details. Note this preference will change the view for all trace files.
