Toolbox | Resequencing Analysis () | Merge Read Mappings ()
This opens a dialog where you can select two or more mapping results, either in the form of tracks or read mappings. If the mappings are based on the same reference sequences (based on the name and length of the reference sequence), the reads will be merged into one mapping. If different reference sequences are used, they will simply be be incorporated into the same result file (either a track or a mapping table).
The output from the merge can either be a track or standard mappings (equivalent to the read mapper's output, see The read mapper tool).
For all the mappings that could be merged, a new mapping will be created. If you have used a mapping table as input, the result will be a mapping table. Note that the consensus sequence is updated to reflect the merge. The consensus voting scheme for the first mapping is used to determine the consensus sequence. This also means that for large mappings, the data processing can be quite demanding for your computer.