Global Viewer pane
The Global Viewer pane for the Mito Alignment viewer shows the coverage depth for the sample. By default, the forward read coverage is displayed in blue and the reverse read coverage in red. A solid black line/hollow black rectangle indicates the pile-up range. By default, green lines indicate the locations of major variants and orange lines indicate the locations of minor variants.
 | The zoom level for the Pile-Up pane determines the appearance of the line/rectangle indicator in the Global Viewer pane. You can change all the default display colors for the Global Viewer pane. See Configuring GeneMarkerHTS Visuals Settings. |
By default, gray shading indicates areas of coverage that fall below the Total Coverage threshold that was specified for the filter settings for the project.
| | For detailed information about the Total Coverage threshold, see To specify the variant call settings for an mtDNA project.“N” is displayed for the consensus sequence in these areas of low coverage in the Consensus Sequence pane. See Reference pane. |
To zoom the display of the Global Viewer pane to only that for the pile-up region, select Zoom Global.
| | For information about the Blocks option and the Variants option, see Pile-Up pane. |
The following options are available for the Global Viewer pane. You can:
• Save the Global Viewer pane display as an image. See To save the Global Viewer pane display as an image.
• Change the default display colors. See To edit the Global Viewer pane colors.