# meaning of ambiguous taxonomic labels in Greengenes

**URL:** <https://forum.qiime2.org/t/meaning-of-ambiguous-taxonomic-labels-in-greengenes/14428>\
**Category:** User Support\
**Tags:** feature-classifier, taxonomy\
**Created:** [April 9, 2020, 11:47pm UTC](https://forum.qiime2.org/t/meaning-of-ambiguous-taxonomic-labels-in-greengenes/14428 "2020-04-09T23:47:23Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Ishanmanandhar](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/i/c68b51/32.png) [@Ishanmanandhar](https://forum.qiime2.org/u/Ishanmanandhar)\
**Post date:** [April 9, 2020, 11:47pm UTC](https://forum.qiime2.org/t/meaning-of-ambiguous-taxonomic-labels-in-greengenes/14428/1 "2020-04-09T23:47:23Z")

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Hello,  
k\_\_Bacteria;p\_\_;c\_\_;o\_\_;f\_\_;g\_\_  
k\_\_Bacteria; **;** ; **;** ;\_\_  
k\_\_Bacteria;p\_\_Actinobacteria;c\_\_MB-A2-108;o\_\_;f\_\_;g\_\_

I have many of these in my taxa file. I am wondering, if I need to filter out the unassigned ones and also, the ones which are distinguished from others but lacking annotations in some taxa levels. How important it to filter out and is there any way to perform this in Qiime2? Some of them are also assigned with unusual names like DS-18, iii1-8 ,does those numbers denote anything(k\_\_Bacteria;p\_\_Acidobacteria;c\_\_iii1-8;o\_\_DS-18) ? To do further analysis like lefse for differntial abundance, is combining all the taxa levels common or should just go with one of the levels?

qiime feature-classifier classify-sklearn --i-classifier gg-13-8-99-515-806-nb-classifier.qza --i-reads rep\_seqs.qza --o-classification taxonomy.qza  
I used gg classifier.

Thanks in advance

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**Author:** ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)\
**Post date:** [April 10, 2020, 8:24pm UTC](https://forum.qiime2.org/t/meaning-of-ambiguous-taxonomic-labels-in-greengenes/14428/2 "2020-04-10T20:24:47Z")

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Hi @Ishanmanandhar,  
Please see this topic for more details about what those different labels mean:

> [@ASV collaps question](https://forum.qiime2.org/t/asv-collaps-question/11764/2):
>
> @shinseung, Those two labels are distinct: The first indicates that the sequence could not be classified beyond kingdom level (which probably indicates that it is really non-bacterial, e.g., host DNA). The second consists entirely of labels from the reference database you used. So QIIME is able to classify that sequence to the genus (or species?) level, but unfortunately the top match is to reference sequence(s) that are totally unannotated in the database. I hope that clarifies!

> [@Ishanmanandhar](#):
>
> How important it to filter out and is there any way to perform this in Qiime2?

I would filter this one but not the others (there is some discussion elsewhere on this forum regarding motivations for this):

> [@Ishanmanandhar](#):
>
> k\_\_Bacteria; **;** ; **;** ;

> [@Ishanmanandhar](#):
>
> Some of them are also assigned with unusual names like DS-18, iii1-8 ,does those numbers denote anything(k\_\_Bacteria;p\_\_Acidobacteria;c\_\_iii1-8;o\_\_DS-18) ?

Probably uncultivated/unknown clades of bacteria, but that nomenclature is specific to the reference database and is not coming from QIIME 2, so you should contact the authors of those databases for more details on their nomenclature.

Good luck!

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**Author:** ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)\
**Post date:** [May 12, 2020, 2:24am UTC](https://forum.qiime2.org/t/meaning-of-ambiguous-taxonomic-labels-in-greengenes/14428/3 "2020-05-12T02:24:49Z")

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