issue with genome wide allele frequencies

[cyadrogarcia]

Good afternoon:
I am new to bioinfirmatic, so please excuse i am asking something very obvious.
I am having a problem when calculateing the genome wide alleles frequencies. In the geno file apparently everything is rigth. However when calculating the allele frequencies the results look very different. please seea fragment:
scaffold position iber int lig mel car sah sicil
Group10 13 0,174,0,0 0,24,0,0 0,8,0,0 0,16,0,0 0,6,0,0 0,13,0,1 0,4,0,0
Group10 26 0,0,0,174 0,0,0,24 0,0,0,8 0,0,0,16 0,0,0,6 0,1,0,13 0,0,0,4
Group10 27 174,0,0,0 24,0,0,0 6,0,0,2 16,0,0,0 0,0,0,6 14,0,0,0 2,0,0,2

Can you provide any clue about how to slve this problem.
Best, Carlos

[simonhmartin]

Hi Carlos,
Please provide the command you used. I assume you are talking about the output of freq.py? If you do not specify --target minor or --target derived, the script will simply output the observed number of each base (A,C,G,T) for each population.
Best wishes,
Simon