Reports

Generate one of three reports for the project: the Coverage report, the Template Length report, or the Read Length report. See Mito Alignment Viewer Reports.

Filter Settings

Opens the Filter Settings dialog box, which contains options for changing the viewer display. See Mito Alignment Viewer Filter Settings.

Load Report

Opens the Load Report dialog box, in which you can select a sample report for display in the viewer. See To save/load reports for an mtDNA project.

Save BAM Edits

If you have made any edits to a BAM project file, then you can save the edited BAM file as a new BAM file.

Save Report

Opens the Save Report dialog box, in which you specify a folder for saving the information that is currently displayed in the Variants table as a report. See To save/load reports for an mtDNA project.

Table Settings

Opens the Table Settings dialog box, which lists all the data columns that are currently displayed in the Variants table of the Mito Alignment viewer. By default, all available columns are initially displayed in the Variants table. To remove a column from the Variants table display, clear its selection. To add a column to the display, select it. See Mito Alignment Viewer Filter Settings.

Toggle Table

Toggles the display (On or Off) of the Variants table in the Mito Alignment viewer. See Variants table.

Export to vcf

Exports all the variants that are displayed in the Pile-up pane to a .vcf file. By default, the .vcf file is named as <sample file name>.vcf and the file is saved in the project folder, but you can edit one or both these values.

EMPOP

Opens the View on EMOP Database dialog box, which lists all the called sample variants for the project by their classification (Major or Minor) on the EMPOP database. See View on EMPOP Database dialog box.