Question

Variant Allele Frequency

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6.3 years ago

kspata ▴ 90

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!!

snp vcf samtools • 1.6k views

ADD COMMENT • link updated 6.3 years ago by btsui ▴ 300 • written 6.3 years ago by kspata ▴ 90

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is a mixed population

You may want to elaborate on what you sequenced.

ADD REPLY • link 6.3 years ago by WouterDeCoster 47k

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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.

ADD REPLY • link 6.3 years ago by kspata ▴ 90

score 2 · Accepted Answer · 2018-08-16

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6.3 years ago

btsui ▴ 300

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.

ADD COMMENT • link 6.3 years ago by btsui ▴ 300