I cant visualise any data on my SNPs table

Im trying to figure out why I cant see any data in the SNPs table of BL , Ive got data in my other sample, L. casei
B. Longum (BL) history

L. casei history

Any help gratefully accepted

Hi @Eleana

Thanks for posting the links, super helpful!

Looking at the outputs from Snippy, these are empty for your BL history – meaning, no variants were called, so there is nothing to visualize later.

That can be for a few reasons: mixed up samples, parameters that are too strict, the quality of the reads, a reference genome that wasn’t assembled as “high quality” yet. You’ll need to investigate to learn which is going on.

Screenshot of your shared history

Hope this helps! :scientist:

Hi there,
Thank you so much for taking the time to reply. Im going to try maybe using Freebayes & perhaps also have parameters not so strict, and hope for the best with this, thanks again

Eleana

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