I have many questions regarding the output of MUMMer's show-diff script. I've read description on
show-diff -h as well as in the README of the top-level directory. However I do not understand the output. I'll start with GAP reported by show-diff.
According to README:
[GAP] A gap between two mutually consistent ordered and
oriented alignments. gap-length-R is the length of the
alignment gap in the reference, gap-length-Q is the length of
the alignment gap in the query, and gap-diff is the difference
between the two gap lengths. If gap-diff is positive, sequence
has been inserted in the reference. If gap-diff is negative,
sequence has been deleted from the reference. If both
gap-length-R and gap-length-Q are negative, the indel is
tandem duplication copy difference.
I made the following illustration trying to understand it.
I do not understand what it means by "If both gap-length-R and gap-length-Q are negative, the indel is tandem duplication copy difference, and how that is different from the reported DUP. Any help is appreciated, thanks.