Freyja plot explanation

[ChromatinLab]

Hello Freyja team,
I have 60 samples from sewage mix data.

I have done WGS using illumina.
I have used Freyja tool for the lineage abundance plotting.

I have used this command :

freyja plot aggregated_filename.tsv

It gave me this plot :

As you can see in this plot, there are so many Delta coming in all samples.
But currently we don't see any Delta trend.
So I request , if you could explain this plot to me for my better understanding of this data it would be very helpful.

Thank you

[joshuailevy]

Hi @ChromatinLab,

I agree, it's a bit unexpected to see Delta popping up at those prevalence levels over the past year or so. The other lineages look more or less like what I'd expect to see in mid/late 2023 though.

Can you provide some info on the specific Delta lineages you're seeing (running plot with the --lineages option will assist with that)? It may also be worth taking a deeper look at the variants outputs from freyja variants to see the specific delta mutations you're observing.

Josh

[ChromatinLab]

Hi Josh,
Thank you for your reply. I have attached the plot here using --lineages option.

Please kindly look into this.

Thank you