# From a newbie: difficulty finding multiple coincident mutations in spike

**URL:** <https://nextstrain.discourse.group/t/from-a-newbie-difficulty-finding-multiple-coincident-mutations-in-spike/373>\
**Category:** Uncategorized\
**Created:** [February 27, 2021, 10:26pm UTC](https://nextstrain.discourse.group/t/from-a-newbie-difficulty-finding-multiple-coincident-mutations-in-spike/373 "2021-02-27T22:26:50Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![earturo](https://avatars.discourse-cdn.com/v4/letter/e/71c47a/32.png) [@earturo](https://nextstrain.discourse.group/u/earturo)\
**Post date:** [February 27, 2021, 10:26pm UTC](https://nextstrain.discourse.group/t/from-a-newbie-difficulty-finding-multiple-coincident-mutations-in-spike/373/1 "2021-02-27T22:26:50Z")

</div>

Using the web-based nextstrain tool using (/ncov/global) I am searching for coincident mutations occurring within the SARS-CoV-2 spike protein S that authors of peer-reviewed literature claim are deposited to GISAID; for example changes to S at positions 261 and 453 from among the Dutch mink sequenced in spring/summer 2020. To do this, I type ‘genotype S 261’ in the Filter Data field and select 261 D from the pull-down menu. From there I see one genome on the genome tree that contains this S sequence change, and none from the Netherlands or among mink where I’d expected them (if I select to filter by mink hosts). Interestingly, if I search for Y453F alone at [covariants.org](http://covariants.org) I can link from there to [auspice](https://nextstrain.org/groups/neherlab/ncov/S.Y453F?c=gt-S_453&f_region=Europe) and filtering this build for G261D does yield mink sequences on the tree, …but when I hover over any of the dotted highlighted genomes, they do not explicitly say that that genome contains a mutation in S at 261 to D. I am new to nextstrain, and I am clearly missing something. Perhaps only the tips of the tree are shown and not the whole list of genomes? If so, how do I change that using the web-based server? Or must I build nextstrain on my local computer? Please help. Any advice is welcome.

---

<div class="post-metadata">

**Author:** ![james](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/james/32/11_2.png) [@james](https://nextstrain.discourse.group/u/james)\
**Post date:** [March 8, 2021, 12:15am UTC](https://nextstrain.discourse.group/t/from-a-newbie-difficulty-finding-multiple-coincident-mutations-in-spike/373/2 "2021-03-08T00:15:27Z")

</div>

Hi @earturo – due to the size of the data available on GISAID, each nextstrain “build” (i.e. each tree) will be showing a subset of the entire dataset – often less than 1% of the total genomes available. Our subsampling strategy depends on the aim of the build – for instance @emmahodcroft’s build [covariants / S.Y435F](https://nextstrain.org/groups/neherlab/ncov/S.Y453F) will preferentially select samples with that mutation whereas [nextstrain / ncov / global](https://nextstrain.org/ncov/global) subsamples geographically.

You can filter the above covariants build to [highlight genomes with a Spike 261D mutation](https://nextstrain.org/groups/neherlab/ncov/S.Y453F?c=gt-S_453&f_region=Europe&gt=S.261D), but again please be aware that this dataset is not representative of all genomes on GISAID.

To explicitly test the claims from your post I believe you’d have to login to GISAID, download all the data, and filter accordingly.