Understanding FREQ; Reasons for variant allele frequency to deviate from 50%

Understanding FREQ; Reasons for variant allele frequency to deviate from 50%

1

What are the reasons to observe variant allele frequency (FREQ) generated on an Illumina DNA sequencing platform around 10-30% or 70-90% for heterozygous variants? As in what are the reasons that this value would deviate from 50%, assuming there is no aneuploidy. Is there any biological mechanism that can explain this or is this just a matter of PCR duplication during sample preparation.

Example:
GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR
0/1:15:28:28:23:5:17.86%:2.5729E-2:32:33:18:5:5:0


DNA


Allele


Frequency

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