Pile-Up pane
Unlike the other panes in the Mito Alignment viewer Panes display, the Pile-Up pane is not explicitly identified by name in the viewer; however, it is always located as the last pane in the display. The pane displays a view of all the reads for the sample as they align to the reference sequence. Greater Than and Less Than symbols point to the 5’ end of the read, where the Greater Than (>) symbol is used for forward reads and the Less Than (<) symbol is used for reverse reads.
Two options that are displayed next to the Global Viewer pane are available for changing the Pile-up pane display:
• Blocks – If Blocks is selected, then the background for each nucleotide is a color and the nucleotide (A, T, C, and G) is white.
• Variants – Selected by default. If Variants is selected, then for all non-variant nucleotides, the background is white and the nucleotide (A, T, C, and G) is displayed in color. For variant nucleotides, the background is colored, and the nucleotide is displayed in white, which is referred to as a highlighted variant.
 | You can select both Blocks and Variants for the Pile-up pane display. In this case, all nucleotides are still displayed in white on a colored background; however, all nucleotides other than variant nucleotides are dimmed and all variant nucleotides are highlighted to visually differentiate them from non-variant nucleotides. To edit the background colors, highlighting colors, nucleotide colors, and the nucleotide visibility for the Pile-up pane display, see To edit the background and highlighting colors in the Pile-up pane display and To edit the visibility and default nucleotide colors for the Pile-up pane display. |