My question is - How many mismatches are allowed (on average/or hard limit) in a bowtie 2 alignment before it moves on to find a new home for a read. I know the we can control the number of mismatches allowed in the seed with -N option. And I know that with the -D option, I control the seed extension attempts that "fail".
So I guess my question now is, when does an extension "fail"? The manual says, when an extension does not yield a new best or a new second-best alignment, it fails.
I'm not able to map this definition to a number (of mismatches). I've re-read the method to calculate the alignment score many times now. Would two consecutive SNPs be allowed, or do two SNPs need to have a certain number of matched bases between them so that the overall alignment doesn't "fail"?
I think, in my naive way, I've explained the core issues of my question. I'll edit if it's not entirely clear.