# Meaning of 'Processed Reads' in Metaphlan4

**URL:** <https://forum.biobakery.org/t/meaning-of-processed-reads-in-metaphlan4/6969>\
**Category:** MetaPhlAn\
**Created:** [April 25, 2024, 3:54pm UTC](https://forum.biobakery.org/t/meaning-of-processed-reads-in-metaphlan4/6969 "2024-04-25T15:54:37Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![PaterJack](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/paterjack/32/2835_2.png) [@PaterJack](https://forum.biobakery.org/u/PaterJack)\
**Post date:** [April 25, 2024, 3:54pm UTC](https://forum.biobakery.org/t/meaning-of-processed-reads-in-metaphlan4/6969/1 "2024-04-25T15:54:37Z")

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Hello,

I have a question related to Metaphlan’ output:

At the top of every .txt files, there’s three lines of commentaries beginning with #. One of them tell us the database used, the next one is the command line, but the final one give the number of “reads processed”.

ex:  
#1311986 reads processed

I know Metaphlan give relative abundances for each clades. What are those lines resuming ? I couldn’t find information about it online, or in the questions here, so I was left wondering:

- is it stricly the number of reads that have a match in the database ?
- is it the number of reads that Metaphlan used for its statistics, whether or not they are counted as contaminant ?
- something else entirely ?

So, more simply put, my question is: What is the definition of “reads processed” in the context of Metaphlan ?

Thank you and regards,

Patrick