Variant Comparison pane
The Variant Comparison (bottom) pane lists the all the variants that were found in at least one sample for the project, where each column is a different sample and the variant percentage for the sample is displayed. The display provides a quick way of visually determining which variants were shared among samples and which were not. Variants that can be classified as a major allele or as a minor allele are highlighted, by default, in blue or gold, respectively. If a variant was determined to be a Low Coverage variant, (the Total Coverage for the variant falls below the Total Coverage threshold that was set for the project), then by default, the variant is highlighted in red.
 | You can change the default highlighting colors that are used in the Variant Comparison pane. See To edit the Comparison viewer variant highlighting colors. |
The following options are available for the Variant Comparison pane.
• Save As: You can click the Save As option that is displayed above the Comparison pane to open the Save Variant Comparison As dialog box and save the information that is displayed in the pane as text (.txt) file with a filename of your choosing. By default, the text file is saved in the same directory as the project, but you can always select a different location.
• Comparison Filter Settings: The specific variants that are initially displayed in the Variant Comparison pane are determined by the filter settings, including the Total Coverage threshold, that were in place at the time that the mtDNA project was saved. To dynamically change the display, on the Comparison viewer main menu, click Comparison Filter Settings to open the Filter Settings dialog box, and make any needed edits. See To specify the variant call settings for an mtDNA project.