**10**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.

**0**• written 4.7 years ago by anikduttapotol •

**10**

Maybe read this, then ask a more specific question if you are still unclear? https://en.wikipedia.org/wiki/Watterson_estimator

4.7k"Please answer as early as possible" sounds suspicious :)

25kWhy would someone answer later than possible....

2.3kHello 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.

0The 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.

1.4k