This links to a question I asked a few days ago (https://www.researchgate.net/post/Is_it_possible_to_get_a_list_of_outlier_markers_from_Arlequin). I want to find out which of my SNPs are outliers according to Arlequin (outliers being those which fall above the 99% quantile line). Therefore does anyone know how Arlequin calculates the Fst values it uses to plot the quantile lines? I know they come from the simulations but how, as far as I am concerned a data set can only have one 99% quantile value?
If I can work out how arelquin is calculating this then perhaps I can work out what the Fst cut off value for each He value I have.
Hi Hazel
From every simulation you perform, you can select/establish the upper 1% and lower 1% (or whatever cut-off value you wish) Fst values for a given He value/range. That is how both confidence limits are selected.
Hope this helps
Pablo
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