Question about -ploidy when mtDNA variants calling

I am puzzling over the polypoid question when I calling snps and indels by GATK in mtDNA re-sequencing data. The polypoid number is not certain due to hundreds of mtDNA in one cell. So, I set -ploidy 100 inorder to call all variants of which frequency >1% using GATK , then there is not only variants with >1% frequency but also variants with <1% frequency (0.25%) in result vcf file. So, why? Is it appropriate that I set -ploidy 100 for mtDNA re-sequencing data analysis.

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