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 methylation, gene expression, copy number, LOH, and mutation 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 that option 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.
	Attribute names are listed at the top of the attribute panel. Colored blocks represent attribute values, where each unique value is assigned a unique color. Hover over a colored block to see the attribute value. Click an attribute name to sort tracks based on that attribute value.