I don't know what is causing this behavior.

Is your bacteria population heterogeneous ?

Do you expect a lot of polymorphic sites at the population level ?


On Tue, 2012-03-06 at 10:44 -0500, Egon Ozer wrote:
> Sorry to keep harping on this, but maybe I found an example of what I
> emailed you about last night, where 1 read sets the consensus over 40
> contradicting reads.  Do you think adjusting my kmer settings up or
> down might minimize this?  At this point I'm not looking for long
> contigs, just the ability to make accurate SNP calls.
> 
> Thanks,
> - Egon
> 
> 
> 



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