# Metaphlan Results Interpretation

**URL:** <https://forum.biobakery.org/t/metaphlan-results-interpretation/8601>\
**Category:** MetaPhlAn\
**Created:** [November 4, 2025, 11:17am UTC](https://forum.biobakery.org/t/metaphlan-results-interpretation/8601 "2025-11-04T11:17:41Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![MichaWeb75](https://avatars.discourse-cdn.com/v4/letter/m/46a35a/32.png) [@MichaWeb75](https://forum.biobakery.org/u/MichaWeb75)\
**Post date:** [November 4, 2025, 11:17am UTC](https://forum.biobakery.org/t/metaphlan-results-interpretation/8601/1 "2025-11-04T11:17:41Z")

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Hi bioBakery community,

I am trying to find out more about the interpretation of MetaPhlan 4.2 results using the paramter -t rel\_ab\_w\_read\_stats.

Using raw reads from pure _Escherichia coli_ sample, I get the following profiles result :

`k __Bacteria|p__ Proteobacteria|c __Gammaproteobacteria|o__ Enterobacterales|f __Enterobacteriaceae|g__ Escherichia|s__Escherichia_coli	2|1224|1236|91347|543|561|562	100.0	0.55438	2741585`

How to interpret the coverage value of 0.55 ? What is the scaling factor of this normalized coverage value ? What is minimum average coverage to identify a marker gene ?

Thanks for your advice!  
Michael

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**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\
**Post date:** [November 4, 2025, 4:45pm UTC](https://forum.biobakery.org/t/metaphlan-results-interpretation/8601/2 "2025-11-04T16:45:02Z")

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0.55438 is the coverage of the clade in reads/(nucleotides of total marker length) units. If you multiply this value by average read length it yields an estimate of the total fold-coverage of the clade. If you multiply this value by average genome length of the clade it estimates the number of reads the clade contributed (that’s the final number in the output, 2741585).

I don’t believe there is a minimum coverage required to detect a marker, but to report a clade in the output, a minimum fraction of its markers needed to recruit 1+ reads (see the `stat_q` parameter in the MetaPhlAn CLI).

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**Author:** ![MichaWeb75](https://avatars.discourse-cdn.com/v4/letter/m/46a35a/32.png) [@MichaWeb75](https://forum.biobakery.org/u/MichaWeb75)\
**Post date:** [November 5, 2025, 11:05am UTC](https://forum.biobakery.org/t/metaphlan-results-interpretation/8601/3 "2025-11-05T11:05:15Z")

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Great . Thanks for the explanations.