Number of alts indicates it could be an autosomal false positive.
Category Variant Annotations
OverviewPotential polymorphic NuMT annotation compares the number of alts to the autosomal coverage
Polymorphic NuMTs (NuMT sequence that is not in the reference) will result in autosomal reads that map to the mitochondria. This annotation notes when the number of alt reads falls within 80% of the autosomal coverage distribution, assuming that autosomal coverage is a Poisson distribution given a central statistic of the depth (median is recommended). This will also include true low allele fraction mitochondrial variants and should be used as an annotation, rather than a filter.
This annotation can only be calculated in Mutect2 if median-autosomal-coverage argument is provided.
GATK version 18.104.22.168 built at Sat, 23 Nov 2019 17:12:18 -0500.