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nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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abnormal bases in recombinations #351

Closed QianGuoPKU closed 1 year ago

QianGuoPKU commented 2 years ago

Hi Nicholas,

I got an average of 1,335,737 recombination bases within the 3,936,291 bp genome. I wonder if the average value is normal or too large. I have noticed that some research excluded genomes with proportions of recombination > 1.0%. Evidently, 1,335,737/3,936,291 (about 1/3) is larger than 1%. Do you have any idea about my issue? Maybe I need to choose another reference genome in the analysis?

Thanks, Qian

nickjcroucher commented 1 year ago

That is a lot of recombination - these samples are probably too divergent to be analysed with Gubbins.