extreme violations of HWE

[renee....@gmail.com]

Hey guys,

Keen on your opinion here. I am working with ddRAD data from AGRF and after I assembled all the data in Stacks, I got 100% of loci with significant departures of HWE using:

HWE_Raw <- gl.report.hwe(x = gl_b,
+                            method_sig = "ChiSquare",
+                            plot.out =  FALSE,
+                            multi_comp_method = "bonferroni")

So then I thought this is crazy, and tested the SNPs called by AGRF, and got the same result.

When I run it with "all" instead of default ("each"), same answer.

When I do a bunch of filtering so I have 90% loci call rate, again, same answer - all loci significantly deviate from HWE. Again, on SNPs by me and by AGRF.

What is the probability that this is true? The data is for the sunset frog (Spicospina flammocaerulea). It's a short range endemic, where initial data looks like there is actually very little migration between individual swamps. Or is this just that I have 10 individuals per swamp and no real power? When i run it on only the pops with 10 individuals I get the same result.

Cheers,

Renee

[Jose Luis Mijangos]

Hi Renee,

By default the function gl.report.hwe only reports loci that significantly depart from HWE. If you want a list with all the loci you should use sig_only = FALSE.

Cheers,

Luis