I am using IDSeq/Nextclade
to identify my SARS-CoV-2 variants and export all the S-protein mutation regions to see what was covered in my reads. We noticed that the E484K and deletion 69-70 regions were not reported in the output. Here is an output for mostly B.1.1.7 and the deletion 69-70 region was not reported. Does Nextclade report these regions?
It’s hard to say definitively why S:E484K is not shown. The mutation is either not present in your sequence, or that region is unsequenced (N).
Can you share the sequence name/accession number with me so I can have a look?
You can see whether the region is sequenced or not by switching to “Gene S” view using the gene view dropdown:
If it’s greyed out, then a region is unsequenced, in my case S:229-289 is unsequenced.
You can check what regions are Ns by hovering over the number in the “Ns” column, then you get a tooltip that will show which regions are Ns:
Deletions are shown in the column called “Gaps”:
I hope that makes things clearer. Let me know if you have any questions.
If you have any particular questions regarding IDSeq, you could try asking here in their repo: GitHub - chanzuckerberg/czid-web: Infectious Disease Sequencing Platform, I’m not familiar with IDSeq, only with Nextclade.