Question about Estimating Pairwise SNV Threshold Using Mutation Rate

[Tonny-zhou]

Dear Author,
Firstly, I would like to express my gratitude for developing this valuable tool for researching recent pathogen transmission. Your work has significantly contributed to the field.
I have a question regarding the estimation of pairwise SNV thresholds using the mutation rate in your example. It appears that the mutation rate should be calculated based on the core genome, correct? If so, shouldn't the calculation of the number of SNVs involve multiplying the mutation rate by the length of the core genome, rather than the entire genome? I noticed that the dataset authors you referenced also used the core genome length for calculating SNPs.
I would greatly appreciate your insights on this matter, as it would help me better understand the methodology applied in your work.
Thank you in advance for your time and consideration. I look forward to hearing from you soon.

Best regards,
Tonny

[esnitkin914]

Hi Tonny,

Sorry for the slow reply - we changed the maintainer of this package. Yes, you are correct that the proper way to do the calculation would be to use the core genome length relative to which variants in your isolate collection were identified.

Best,

Evan