# Explanation of the output of phylophlan\_metagenomic **URL:** \ **Category:** PhyloPhlAn\ **Created:** [January 21, 2021, 2:21pm UTC](https://forum.biobakery.org/t/explanation-of-the-output-of-phylophlan-metagenomic/1588 "2021-01-21T14:21:19Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![BioMickWatson](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/biomickwatson/32/359_2.png) [@BioMickWatson](https://forum.biobakery.org/u/BioMickWatson)\ **Post date:** [January 21, 2021, 2:21pm UTC](https://forum.biobakery.org/t/explanation-of-the-output-of-phylophlan-metagenomic/1588/1 "2021-01-21T14:21:19Z")
Hello! I am a bit confused about the output of phylophlan\_metagenomic. For example, I have run it with a novel MAG and it gives me: ``` uSGB_48157:Family:k __Bacteria|p__ Actinobacteria|c __Actinobacteria|o__ Geodermatophilales|f __Geodermatophilaceae|g__ GGB33989|s __GGB33989_SGB48157|t__ SGB48157:0.0247779 uSGB_48156:Other:k __Bacteria|p__ Bacteroidetes|c __CFGB14357|o__ OFGB14357|f __FGB14357|g__ GGB39511|s __GGB39511_SGB48156|t__ SGB48156:0.276697 uSGB_48155:Genus:k __Bacteria|p__ Proteobacteria|c __Alphaproteobacteria|o__ Rhodobacterales|f __Rhodobacteraceae|g__ Stappia|s __Stappia_SGB48155|t__ SGB48155:0.295981 ``` So the first one, the taxon level is “Family”, the second one “Other”, the third one “Genus” - what does this mean? I guess the 0.0247779 means the MAG is about 2.5% MASH distance from uSGB\_48157, are you telling me that this is a Family level assignment because that SGB only has a proper name down to Family level? What does “Other” mean for the second result? This has a name at Phylum level. Is there somewhere that explains the output of phylophlan\_metagenomic? Thanks Mick ---
**Author:** ![f.asnicar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/f.asnicar/32/196_2.png) [@f.asnicar](https://forum.biobakery.org/u/f.asnicar)\ **Post date:** [January 21, 2021, 4:29pm UTC](https://forum.biobakery.org/t/explanation-of-the-output-of-phylophlan-metagenomic/1588/2 "2021-01-21T16:29:32Z")
Hello Mick, thank you for your message. We do have a part of the wiki trying to explain the output here: [Home · biobakery/phylophlan Wiki · GitHub](https://github.com/biobakery/phylophlan/wiki#output-description) But let me try to explain it again here as this could also be found by others in the future. your output file should resemble the following: ```auto my_bin (k|u)SGB_ID:taxa_level:taxonomy:average_mash_distance [(k|u)SGB_ID:taxa_level:taxonomy:average_mash_distance] ``` And you’ll find as many ```auto (k|u)SGB_ID:taxa_level:taxonomy:average_mash_distance ``` columns as specified by the `-n/--how_many` param (10 is the default). This list of columns are sorted by their `average_mash_distance`, so the first one will be the closest. Now, for the other parts: - `my_bin` will be the name of your input genome/MAG - `(k|u)SGB_ID`: will tell you the SGB ID (`ID`) and `k` or `u` indicate whether it is a known (`k`) or an unknown (`u`) SGB. This follows the rule we used in this [work](https://doi.org/10.1016/j.cell.2019.01.001), where `kSGB` are those that contain a reference genome deposited in public databases (filtered a bit, not just all genomes in NCBI) and `uSGB` will only contain MAGs. - `taxa_level`: can be either `Species`, `Genus`, `Family`, or `Other`, depending at which taxonomic level the SGB has been assigned to. Where `Species` will only be used for kSGBs practically because only those will have a taxonomic label assigned at the species level within the SGB. `Genus`, `Family` and `Other` are for the uSGB to indicate (to put it very simply) how “far” a reference genome is found. `Genus` means that the GGB that SGB belongs to contains a reference genomes and hence its taxonomic label is used up-to the genus level. `Family` similarly but the reasoning is done at the FGB level up-to the family taxonomic level. `Other` instead it means that both GGB and FGB assigned to that SGB are both unknown (hence an uGGB and uFGB, respectively). In this case, we report it as `Other` and the taxonomic label is retrieved by taking the one assigned to the closest reference genome. - `taxonomy`: is the full taxonomic label assigned to the SGB - `average_mash_distance`: is the average Mash distance of the input bin w.r.t. all the genomes in the SGB. Like in your case, about 2.5% average Mash distance from all the MAGs in the uSGB\_48157. In your case, both uSGB\_48156 and uSGB\_48155 are too distant to consider your MAG as a potential new member of them because their Mash average distance is \>5%. While it appears that your MAG is a new member of uSGB\_48157 with an average Mash distance of ~2.5%. Sorry for the long message, but I hope this helps. Many thanks, Francesco ---
**Author:** ![BioMickWatson](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/biomickwatson/32/359_2.png) [@BioMickWatson](https://forum.biobakery.org/u/BioMickWatson)\ **Post date:** [January 21, 2021, 4:35pm UTC](https://forum.biobakery.org/t/explanation-of-the-output-of-phylophlan-metagenomic/1588/3 "2021-01-21T16:35:07Z")
Hi Francesco Thank you so much for your explanation, and I must apologise for missing the explanation on the wiki, it’s very bad of me to ask a question that has already been answered! Many thanks for your patience Mick ---
**Author:** ![LPrunus](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/lprunus/32/2788_2.png) [@LPrunus](https://forum.biobakery.org/u/LPrunus)\ **Post date:** [February 10, 2025, 1:36pm UTC](https://forum.biobakery.org/t/explanation-of-the-output-of-phylophlan-metagenomic/1588/4 "2025-02-10T13:36:17Z")
Hi Francesco, I actually also have a question concerning this output. Some of my bins get classified as “SGB\_ID\_group”. So if I use for example the **phylophlan\_draw\_metagenomic** function, these get labelled in the heatmap as _unassigned_. Example: kSGB\_14816\_group:Species:k\_\_Bacteria|p\_\_Actinobacteria|c\_\_Coriobacteriia|o\_\_Eggerthellales|f\_\_Eggerthellaceae|g\_\_Ellagibacter|s\_\_Ellagibacter\_isourolithinifaciens|t\_\_SGB14816:0.04177145460526316 - What does this \_group classification mean? - Why are they unassigned, although being classified on species level? (or other level, I also get this for uSGBs) I hope I did not miss an explanation somewhere. Thank you in advance! Best, Lydia