Understanding MUMmer show-diff
0
1
Entering edit mode
6.2 years ago
Huggie ▴ 20

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.

MUMMer • 2.9k views
ADD COMMENT
0
Entering edit mode

Hello,Huggie,

Did you find the answer?

ADD REPLY

Login before adding your answer.

Traffic: 1732 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6