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.

Hello,Huggie,

Did you find the answer?