Zero or low coverage regions in a Reads Track (read mapping in track format) can be identified and annotated using the following tools.

First use the Reads track as input for:

Toolbox | Utility Tools | Tracks | Graphs | Create Mapping Graph 

to create a Mapping Graph Track.

Then use the Mapping Graph Track as input for:
 

Toolbox | Utility Tools | Tracks | Graphs | Identify Graph Threshold Areas
 

In this tool you can set the minimum and maximum coverage to look for. This tool will then generate an annotation track with regions having the specified coverage.

The tools are described in detail on the following manual pages:

Create Mapping Graph
Identify Graph Threshold Areas

Below you see an example image of a track list including a Reads Track and the track outputs of the tools above, where the aim was to identify low coverage areas in the mapping. 

By opening the track containing the low coverage annotations in table view, you can see information, like the coordinates of the annotations. From within a track list, you can open a particular annotation track in table view by clicking on the table icon or double clicking on the name of the track.