AF column in results and HWE

[medinacarolina]

Dear Xiaowei, I was looking at the columns in my rvtest output but somehow the AF (I guess standing for allele frequency) does not match with the report in the columns N_REF, N_HET and N_ALT.

For example

N_REF=1200; N_HET=125; N_ALT=0; reports in the AF column 0.305

How could this be? from my manual calculation Freq_REF=0.953 and Freq_Alt=1-0.953

Also, the reported HWE Pval is 0.11, how could this be?

I have done the excercise for 17 SNPs (header of one of my files and none of the AF was similar to the reported one
caro_rvtest.xlsx