# Resource for representative nucleotide changes for Nextstrain clades

**URL:** <https://nextstrain.discourse.group/t/resource-for-representative-nucleotide-changes-for-nextstrain-clades/1698>\
**Category:** General\
**Created:** [July 24, 2024, 9:16am UTC](https://nextstrain.discourse.group/t/resource-for-representative-nucleotide-changes-for-nextstrain-clades/1698 "2024-07-24T09:16:06Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![meadow](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/meadow/32/626_2.png) [@meadow](https://nextstrain.discourse.group/u/meadow)\
**Post date:** [July 24, 2024, 9:16am UTC](https://nextstrain.discourse.group/t/resource-for-representative-nucleotide-changes-for-nextstrain-clades/1698/1 "2024-07-24T09:16:06Z")

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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](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv).  
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](http://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!

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<div class="post-metadata">

**Author:** ![rneher](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/rneher/32/20_2.png) [@rneher](https://nextstrain.discourse.group/u/rneher)\
**Post date:** [August 2, 2024, 11:17pm UTC](https://nextstrain.discourse.group/t/resource-for-representative-nucleotide-changes-for-nextstrain-clades/1698/2 "2024-08-02T23:17:33Z")

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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

> **[GitHub - corneliusroemer/pango-sequences: Consensus sequences for each Pango lineage](https://github.com/corneliusroemer/pango-sequences)**
>
> Consensus sequences for each Pango lineage

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