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Published 20 hours ago • verified publisher icon nextstrain

ENH: Display location of SNP cluster somewhere in web

Open corneliusroemer opened this issue 2 years ago • 4 comments

I have a sequence that's reported to have 11 mutations in a cluster, but I can't figure out where this cluster is supposed to be.

It would be helpful in these situations if the location of the cluster was displayed somewhere, possibly in the QC tooltip.

image

corneliusroemer avatar Jan 26 '22 16:01 corneliusroemer

Or is this a bug? I can't possibly find a cluster with width 100 and 11(!) private muts there, even a window of 1000 wouldn't be enough.

image

corneliusroemer avatar Jan 26 '22 16:01 corneliusroemer

I think I've figured it out: private deletion reversions are counted as individual private mutations. So if you have a stretch of 9 deletions plus 2 other private muts you get to 11.

I think this is a bug, possibly because of new private mut feature. Will open as new issue.

corneliusroemer avatar Jan 26 '22 16:01 corneliusroemer

~@corneliusroemer Is this issue the same as https://github.com/nextstrain/nextclade/issues/707? Does it require any work additional to https://github.com/nextstrain/nextclade/pull/710?~

Sorry, I see now. The feature request is to display SNP clusters.

ivan-aksamentov avatar Jan 27 '22 20:01 ivan-aksamentov

Yes, sorry, I've hidden the off topic comments that spawned the new issue.

corneliusroemer avatar Jan 27 '22 21:01 corneliusroemer