Reasonable number of SNPs in a bacterial genome.

Question

[yesquokkan]

Hello,

I am looking for SNPs in a specific bacterial species genome.

How can I determine whether the number of SNPs detected in my dataset is reasonable?

I understand that the expected number of SNPs can vary by species, but how can I establish an appropriate baseline or reference for the species I’m studying?

Thank you in advance.

[dthorbur]

There are a lot of factors that can impact the number of identified SNPs. These include things like:

• Evolutionary distance from sample to reference genome
• Type and intensity of selection acting on sample population
• Species specific factors like efficiency of DNA repair machinery
• Sequencing methodology and depth

The list goes on. So finding an expected number would likely require someone knowledgeable with the specific system and species you are using.

[michael.ante]

If your bacterial species is a (human) pathogen, you might want to check outbreak analysis papers of that species.

In general, you find there how many SNPs are reasonable to define 2 assemblies as being part of a single source.