Non-specific matches

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:

Note that a read is only considered non-specific when the read matches equally well at several alignment positions. For example, if there are two possible alignment positions and one of them is a perfect match and the other involves a mismatch, the read is placed at the position with the perfect match and it is not marked as a non-specific match.

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.