# Per read assignment

**URL:** <https://forum.biobakery.org/t/per-read-assignment/3237>\
**Category:** MetaPhlAn\
**Created:** [March 1, 2022, 12:19am UTC](https://forum.biobakery.org/t/per-read-assignment/3237 "2022-03-01T00:19:53Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Bhav\_Verma](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/bhav_verma/32/1277_2.png) [@Bhav\_Verma](https://forum.biobakery.org/u/Bhav_Verma)\
**Post date:** [March 1, 2022, 12:19am UTC](https://forum.biobakery.org/t/per-read-assignment/3237/1 "2022-03-01T00:19:53Z")

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Hey Guys,

Thanks for the great tool. I was wondering if I could get per read marker gene assignment.

Specifically, I have 1000000 reads but only 26000 are mapped in the Bowtie file. It’s also a similar thing with your example files on the wiki. Is it because a large subset of these reads were not mapped to marker genes?

My ideal goal would be to have a taxon and/or a marker gene per read that could be mapped to a taxon. Is this possible with MetaPhlan or should I just expect a large subset of reads can’t be mapped to a taxon?

Thanks!

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**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [May 18, 2022, 3:06pm UTC](https://forum.biobakery.org/t/per-read-assignment/3237/2 "2022-05-18T15:06:13Z")

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Hi @Bhav_Verma  
Thanks for getting in touch. As you mention, the MetaPhlAn database only contains the species-specific marker genes (maximum 150 genes per species), so the numbers you are reporting are totally expected.