At the bottom of the dialog, you can specify how Non-specific matches should be treated. The concept of Non-specific matches refers to a situation where a read aligns at more than one position with an equally good score. In this case you have two options:
- Random. This will place the read in one of the positions randomly.
- Ignore. This will not include the read in the final mapping.
For paired data, reads are only considered non-specific matches if the entire pair could be mapped elsewhere with equal scores for both reads, or if the pair is broken in which case a read can be categorized as non-specific in the same way as single reads (see Mapping paired reads).
When looking at the mapping, the default color for non-specific matches is yellow.