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! 
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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