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Which cut-off does GATK use to determine 'background-noise'?

I've just begun working with GATK. I've done an analysis with a mitochondrium (not human) and now I'd like to know:
firstly: When does GATK list a variation? I have only few positions where less than 1% of the reads have a variation, and no positions where there are less than 0.5% listed. So what exactly is listed as a variation? (Information: I've skipped the deduping step, as we want to have many reads due to high variation within mitochondria, the average coverage is about 50 000)
secondly: Sometimes the VCF-file has, instead of 1/1/1/1... only ./././ and no information about the actual reads. What does that mean?
Is there a possbility that I could just get the amount of reference and alternative base(s) without any 'censoring'?

I'm rather confused about how all of this works, especially in the light of mitochondrial variation analysis.

I hope you guys can help me!

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