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xavierdidelot / ClonalFrameML

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
GNU General Public License v3.0
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why the r/m I calculated is so small using a subclone of subclone of klebsiella pneumoniae #134

Closed xuechunxu closed 2 years ago

xuechunxu commented 2 years ago

Hi Torsten, I used a set of genomes from KL subclone of ST subclone of klebsiella pneumonia to calculate their recombination. The r/m is very small. I guess it is because my genomes are very similar and the diversity is low, but I am not sure. Is this result accurate? image

Thanks ChunXu

xavierdidelot commented 2 years ago

Hi ChunXu,

I can confirm that your calculation is correct, ie r/m=(R/theta)deltanu The values of delta and nu are reasonable, but the values of R/theta are very low, which is why you get such low r/m.

Best wishes, Xavier