MacVector tries to optimize the Map graphics layout using a trade-off between performance and minimizing unnecessary white space. Sometimes the default settings we have chosen are not ideal, particularly if you are looking at the Map tab of an Align To Reference window where you have a large number of reads overlapping the same region. To clean up these views, you can increase the number of graphical levels using the MacVector Preferences | Map View tab.
For more information on the use of levels in the Map tab, please checkout this blog post.
