IGV supplements each alignment track with (1) a coverage track and (2) if selected in the Alignment Preferences panel, a default splice junctions track. This section pertains to the default junctions track as well as to independently loaded junctions data. For plots that can provide more detailed junction information, see Sashimi Plots.
Each splice junction is represented by an arc from the beginning to the end of the junction.
Hovering the mouse over a junction will display the coverage. The first screenshot shows multiple coverage detail panels for each three components of two splice junctions on opposite strands.
Enable junctions view for .bed files
The splice junction view displays an alternative representation of .bed files encoding splice junctions, such as the "junctions.bed" file produced by the TopHat program. Display details are as described in the section above.
The track can also be computed dynamically from an Alignment track by enabling the Show splice junctions track option in the alignment preferences as described above.
Junction files should be in the standard .bed format. The score field is used to indicate depth of coverage.