Resource for representative nucleotide changes for Nextstrain clades

General
1

Hello all,

Firstly, thanks for the contribution to the field with Nextstrain and all the associated resources!

We would like to use Nextstrain resources in our project, and I have been digging into your resources for a while.

However, after spending quite a lot of hours (please excuse me if my words are conceptually not so correct as I’m a newbie in the virus world), I do not seem to understand how I can create a resource that contains all the mutations that each Nextstrain clade contains for SARS-CoV-2. Here I must state that I am not looking for defining mutations like Nextstrain uses for augur clades to define clades on the tree: ncov/defaults/clades.tsv at master · nextstrain/ncov · GitHub.
What I am looking for is a set of all the mutations that each clade contains.
In Nextclade CLI, I came across tree.json for SARS-CoV-2 among dataset files. It seems to contain all clades with nucleotide changes but I have realized it’s not inclusive enough when I compared individual clades with the mutations shown in covariants.org plus it’s also not the same with what’s offered with clades.tsv.
I have looked up a lot and I did not find a resource that I could extract all mutations for each clade.
I would be very glad if anybody could give me any ideas or some insights on my problem.

Thank you in advance!

2

To obtain the mutations of a particular clade from the tree.json, you need to accumulate all mutations on the path from the root to the sequence/node of interest. This then includes all mutations and deletion, but not the insertions.

another resource would be the pango-lineage consensus sequences maintained by @corneliusroemer

If you compare these to the reference, you can read off all mutations.