If you have imported data from variant databases into NextGENe, then the Alignment Viewer displays one or more Track panes, with one pane for each track that has been queried for the project. Tic marks indicate positions in each track for which there is information. If Set Amplicon BED File was selected in the Load Data step of the Project Wizard for the loaded project, then the amplicon ROIs are displayed as a solid pink link in the ROI pane for the section.