What is a samtools mpileup reference skip? The samtools documentation for mpileup states:


  At this column, a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand, a '>' or '&lt;' for a reference skip
  ...
  Similarly, a pattern `-[0-9]+[ACGTNacgtn]+' represents a deletion from the reference.


What is a reference skip?
That documentation has been expanded recently (see PR #1055) and now describes the characters seen in this column in more detail:

Forward   Reverse                    Meaning
---------------------------------------------------------------
 . dot    , comma   Base matches the reference base
 ACGTN     acgtn    Base is a mismatch to the reference base
   &gt;         &lt;      Reference skip (due to CIGAR "N")
   *         *      Deletion of the reference base (CIGAR "D")


(And so on — see the pull request or doc/samtools-mpileup.1 on the develop branch for the complete pileup format description. The documentation on that web page will be updated when this is released in a new samtools release.)

As noted in https://bioinformatics.stackexchange.com/a/421/134, SAM has always had separate D (deletion from the reference) and N (skipped region from the reference) operators. These are treated similarly computationally but emitted intentionally by aligners to distinguish introns and the like from other deletions.