Hi, What is the difference between the Pango lineage (nextclade) and the unaliased?

@lucyintheskyzzz Pango lineages sometimes go a bit crazy, like B.1.23.456.7.89, so at some point Pango folks invented aliases. In Nextclade the "lineage" column nowadays shows the alias and "unaliased" column shows either partially aliased or canonical lineage, i.e. with aliasing cancelled to some degree or entirely.

You can see how aliases are helpful on some of the example sequences:
https://clades.nextstrain.org/?dataset-name=sars-cov-2&input-fasta=example
Sort by "Pango lineage" and scroll to rows containing "AY" lineages

This is not related to Nextclade itself. Aliases is a Pango thing and Nextclade mimics Pango. But yes, our column names are a bit backwards (for legacy reasons) and perhaps our usage of the jargon term "unaliased" is a bit frivolous.

Hi @ivan-aksamentov do you know where I can find if my sample had del 69-70?

@lucyintheskyzzz If you mouse-hover a value in the column "Del", a tooltip will show up displaying a list of nucleotide deletions and a list of aminoacid deletions. If S:H69- and S:V70- are in the list, then Nextclade detected these deletions in your sample. Note that if your sequence is incomplete (missing this particular region) or has non-ACGT nucleotides in this region, Nextclade will be unable to detect deletions there and they will not show up.

Alternatively, you can mouse-hover the black markers in sequence view (last column) and, if detected, deletions will also be displayed there:

You can also download the TSV output file:

and open it in Excel, Google Sheets or other spreadheet software or analyze it programmatically. The aaDeletions column will contain all detected aminoacid deletions:

Finally, you can download translated polypeptide sequences (in fasta format) and open them in any alignment viewer software (such as AliView or https://alignmentviewer.org/) and then see if columns 69 and 70 has - in them:

P.S. I suggest you open a new issue for each question, suggestion or bug report, or join our discussion forum (https://discussion.nextstrain.org), instead of posting into unrelated issues. This will make it easier for developers and other users to navigate in GitHub issues.

OK thanks!