The names of aligned sequences in mature groups adhere to a naming convention that generates unique names for all isomiRs. This convention is inspired by the discussion available here: http://github.com/miRTop/incubator/blob/master/isomirs/isomir_naming.md
Deletions are in lowercase and there is a suffix s for 5' deletions (figure 16.9):
Insertions are in uppercase and there is a suffix s for 5' insertions (figure 16.10):
Note that indels within miRNAs are not supported.
Mutations (SNVs) are indicated with reference symbol, position and new symbol. Consecutive mutations will not be merged into MNVs. The position is relative to the reference, so preceding (5') indels will not offset it (figure 16.11):
Deletions followed by insertions will be annotated as shown in figure 16.12:
If a sequence maps to multiple miRBase entries or to multiple entries in a custom database, we will add the suffix `ambiguous' to its name. This can happen when multiple species are selected, as they will often share the same miRBase (or other reference) sequence, or when a read does not map perfectly to any miRBase entry, but is close to two or more entries, distinguished by just one SNV, for example.