Variant Allele Frequency
Hi,
I have used samtools to find variants for a sample using reference sequence. I have found some Indels at 10%, 80% and 100% frequency.
Can I interpret in this case that the variant with 10% frequency has 90% of the reads identical to reference sequence and is a mixed population?
Thanks in advance!!
1 answer
Q: Can I interpret in this case that the variant with 10% frequency has 90% of the reads identical to reference sequence and is a mixed population?
A: You might want to check the base quality, to make sure it is not sequencing error. Other than that, it could be due to contaminants too.
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You may want to elaborate on what you sequenced.
I sequenced a NGS library prep of plasmid DNA samples prepared from cell cultures. I was provided with purified DNA which was sequenced on Illumina MiSeq PE 300.