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!
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written
by
polangxin •
1 answer
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.
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