Consensus pane
The Consensus pane displays the consensus sequence for the major alleles, where a major allele is defined as the allele with the highest frequency at a given position. If any areas of coverage fall below the Total Coverage threshold that was specified for the project filter settings, then the consensus sequence is set to “N” for these regions in the pane.
 | For detailed information about the Total Coverage threshold, see To specify the variant call settings for an mtDNA project. The corresponding areas of low coverage are highlighted in gray in the Global Viewer pane. See Global Viewer pane. |
You can right-click anywhere in the Consensus pane to open a context menu with two options for copying the consensus sequence.
• Copy Consensus. Opens the Copy Consensus dialog box. The dialog box displays the start and end positions for the portion of the consensus sequence that is currently displayed in the Consensus pane.
The following options are available for the Copy Consensus dialog box:
• You can leave the Start and End positions as-is, or you can manually edit the values.
• You can copy the consensus sequence bases as displayed (G, A, etc.) or you can select Use IUPAC to copy the consensus sequence in its IUAPC nomenclature code instead.
• You can select Copy to copy the designated region for the sequence (start and end positions are included) to the client clipboard, or you can click Copy All to copy the entire consensus sequence, regardless of the Start and End positions that are indicated, to the client clipboard. You can now paste the copied information into a third-party application such as Microsoft Excel.
• Copy Entire Consensus. Copies the entire consensus sequence to the client clipboard. You can now paste the copied information into a third-party application such as Microsoft Excel.