Mutect FA = 0 when variant Pass

Hi

I have used mutect-1.1.7, and after filtering the variants that do pass HC filters I'm looking at the frequency of the alleles. Some alleles show a frequency different from 0, but lots of them show a frequency of 0. I do not understand why this is 0 when it should be different from 0.

Example

GT:AD:BQ:DP:FA:SS 0:39,0:.:39:0.00:0

Thanks.

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