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barricklab / breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
http://barricklab.org/breseq
GNU General Public License v2.0
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Problem in understanding breseq output (26-bp)2→1 #358

Closed Subhajeet1997 closed 9 months ago

Subhajeet1997 commented 9 months ago

image what this (26-bp)2→1 actually means?

jeffreybarrick commented 9 months ago

There was a tandem repeat of 2x26 base pairs in the reference (26 bp then the same 26 bp again right after it). In the sample, only one copy of the repeat is detected (one was deleted).

So, it's a 26-bp deletion, but breseq gives you some extra info that a tandem repeat was involved.