To edit the visibility and default nucleotide colors for the Pile-up pane display
In the Sample Viewer sub-pane, you specify the variant visibility and the nucleotide colors in the Pile-up pane display for the Mito Alignment viewer.
• Variant Visibility. Determines how dimmed non-variant nucleotides are when compared to the variant nucleotides when both Variants and Blocks are selected for the pane display in the Mito Alignment viewer. The default value is 40%.
• The sub-pane also displays the various colors that are to be used in the Pane displays where the default nucleotide colors are the following:
• For non-variant nucleotides and SNPs: If Variants is selected, then Green, Blue, Black, and Red indicate the colors for the nucleotides A, C, G, and T, respectively. If Blocks is selected, then these indicate the colors for the nucleotide backgrounds.
• For Deletions: No nucleotide is displayed. Instead, a burnt orange dash is displayed.
• For Insertions: If Variants is selected, then the nucleotide is displayed in purple. If Blocks is selected, then the nucleotide background is purple.
• If coverage areas fall below the Total Coverage value that is specified for the Filter Settings: If Variants is selected, then a gray “N” is displayed for the consensus sequence in these regions. If Blocks is selected, then the nucleotide background is displayed in gray and “N” is displayed in white.
1. On the Application Settings dialog box, ensure that the Global Viewer sub-pane is visible.
2. Do any or all of the following as needed to edit the variant visibility and/or change colors
• Adjust the value for Variant Visibility.
• To make the non-variant nucleotides more visible in the pane display when both Blocks and Variants are selected, increase the value.
• Conversely, to make the non-variant nucleotides less visible in the pane display when both Blocks and Variants are selected, decrease the value. You can manually enter a new value, or you can use the Up/Down arrows.
• Change one or more colors for the nucleotides and/or variants. To do so, double-click the color swatch that is displayed for a nucleotide or variant type to open the Select Color dialog box, select a different color, and then click OK.
The Select Color dialog box closes and the Application Settings dialog box remains open. The newly selected color is displayed for the selected nucleotide or variant type.
3. Do one of the following:
• If you are done specifying your settings, then click Save to close the Application Settings dialog box and return to the GeneMarkerHTS main window.
• Continue to edit other application settings as needed.