Let's say we have the following situation.
We have a unique breakpoint in mtDNA (a deletion in the mtDNA). If by chance this molecule is replicated and now this unique molecule exist as multiple copies.
How would delly handle this situation? Can it distungish how many molecules exits in the sample? if by counting this unique breakpoint only once with the software, is it be possible that we are not considering the abundance of this unique breakpoint.
I would appreciate any hints also as to where I can look it up.