I have two populations, CEU and CHS, and 50 individuals for each populations.
I split each chromosome into segments with 100kb window size.
For each individual, there are some some bins(100bp) in each window.
Now, I hope to know, for each window, whether the total number of bins is significant difference between two populations or not.
In such case, which hypothesis test is best ?
I think, in this case, the mean value is not very meaningful, so I do not choose two samples t test.
Is there any other better methods?