Main Window

The following figure shows data from The Cancer Genome Atlas:

The tool bar provides access to commonly used functions. The menu bar and pop-up menus (not shown) provide access to all other functions.

The red box on the chromosome ideogram indicates which portion of the chromosome is displayed. When zoomed out to display the full chromosome, the red box disappears from the ideogram.

The ruler reflects the visible portion of the chromosome. The tick marks indicate chromosome locations. The span lists the number of bases currently displayed.

IGV displays data in horizontal rows called tracks. Typically, each track represents one sample or experiment. This example shows segmented copy number data.

IGV also displays features, such as genes, in tracks. By default, IGV displays data in one panel and features in another, as shown here. Drag-and-drop a track name to move a track from one panel to another. Combine data and feature panels by selecting the option to display all tracks in a single panel on the General tab of the Preferences window.
Track names are listed in the far left panel. Legibility of the names depends on the height of the tracks; i.e., the smaller the track the less legible the name.
An optional attribute panel displays sample/track attributes represented as colored blocks, where each unique value is assigned a unique color.