Question: Watterson's estimator "theta"
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anikduttapotol10 wrote:

Hello,

Can anybody tell me what does watterson's estimator theta mean? I have got a value of 0.17 for theta from my simulated SNP data. Now how can I explain this? Please answer as early as possible.

snp • 8.0k views
modified 3.5 years ago by Zeinab 0 • written 4.7 years ago by anikduttapotol10
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Maybe read this, then ask a more specific question if you are still unclear? https://en.wikipedia.org/wiki/Watterson_estimator

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Why would someone answer later than possible....

Hello everyone, It is an old post, but I ask my question here because I have pretty much the same problem. I do not really know how to interpret the Watterson's estimator. To be specific, I do not understand what the denumerator is for. Wikipedia says that this correction factor is used to take into account that the number of segregating sites increase with an increasing sequence length. But why do we use this strange factor and do not just divide the number of segregating sites by the total number of sites? I hope someone can help me out because this factor is driving me nuts. It seems like it is so trivial for everyone that it is impossible to find an explanation.

The simple answer is that the estimator is a ratio of observed SNP sites versus what we would expect to occur given a neutral model of evolution (that expectation is the denominator value).

As to why it's there: the harmonic numbers are part of the solution to expectation in counting problems (those that are modeled as Poisson processes, such as this one). You can read more about it here.

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155358560310 wrote:

Watterson's estimator theta，a parameter of nucleotide diversity，depends on the SNP number and population size. A single value is useless. Ask a more specific question.

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Zeinab 0 wrote:

Hi I will be very grateful if you are so kind answer me about 2 question from population differentiation method. 1- What can be interpreted from a negative Theta value (-1) when measuring pairwise Theta value (Fst) between 2 populations? 2- I have 2 animal breeds with several sub-populations. I analyse my data with Theta value in 2 breeds and their sub-populations. Why Theta value is different between sub-populations and breeds?? for subpopulations must analysis with Fsc value????