How To Calculate Genome Clock Rate From Snp'S Clock Rate

Question

[polangxin]

a lot of sample mapping to 1 genome(as reference), call snps, then join them as a Multiple Sequenc Aligenment file, use BEAST calculate the clock.rate is 9e-4.

the ref is about 40000bp, and SNPs is 6000.

i think 9e-4 is the snps' clock rate, am i right? then how i calcute the specie's clock rate?

Thank!

Answer 1

[Lee Katz]

You are close. I am assuming that you got the clock rate from Tracer or something comparable. Next you'll have to consider the search space. If you start with 6kb out of 40kb, then I believe that you will need to multiply your clock rate by 6/40. 9E-4*6/40=0.000135 snps/genome/unit time.

Please anyone, correct me if I am wrong. I haven't had to do this yet but it makes sense to me, conceptually.