Hello i would like to understand something. I get the metagenome profile txt output with the relative abundances for the taxonomies it provides.
Why there is a number of additional species without any relative abundances given?
how can i provide relative abundances for these species ?
does metaphlan 3.0 just provide some other species that putatively exist in the sample but their statistical significance according to the vector of markers on their clade is not adequate?
is there a relative abundance threshold that they do not reach so they are just reported as additional species?
it is an important issue as it can alter the results of the profile quite a lot.
also, when i get the marker relative abundances how can i see the taxonomic level that they refer to? because i understand from looking at their ids at the chocophlan marker ids database v30 , they can be anything from all the taxonomy of a species up to the kingdom of bacteria. So i understand i cannot just infer the taxonomic level from the marker relative abundances of a clade.
i d appreciate if you shed some light on the matter. thanks a lot in advance
i post the result of the metagenomic profile
#mpa_v30_CHOCOPhlAn_201901
#SampleID Metaphlan_Analysis
#clade_name NCBI_tax_id relative_abundance additional_species
UNKNOWN -1 99.99916
k__Bacteria 2 0.000841731043728058
k__Bacteria|p__Bacteroidetes 2|976 0.0007007640731611021
k__Bacteria|p__Actinobacteria 2|201174 0.00014096697056695595
k__Bacteria|p__Bacteroidetes|c__Flavobacteriia 2|976|117743 0.0007007640731611021
k__Bacteria|p__Actinobacteria|c__Actinobacteria 2|201174|1760 0.00014096697056695595
k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales 2|976|117743|200644 0.0007007640731611021
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales 2|201174|1760|85009 0.00014096697056695595
k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae 2|976|117743|200644|49546 0.0007007640731611021
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae 2|201174|1760|85009|31957 0.00014096697056695595
k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flagellimonas 2|976|117743|200644|49546|444459 0.0007007640731611021
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium 2|201174|1760|85009|31957|1912216 0.00014096697056695595
k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Flagellimonas|s__Flagellimonas_sp_HME9304 2|976|117743|200644|49546|444459|1383885 0.0007007640731611021
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes 2|201174|1760|85009|31957|1912216|1747 0.00014096697056695595 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_CC003_HC2,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_KPL2009,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_CG1_02_60_36,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_HMSC069G10,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_HMSC068C01,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_KPL1849,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_HMSC078F10,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_HMSC067A02,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_KPL2008,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_KPL1854,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_434_HC2,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_409_HC1,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_5_U_42AFAA,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_HMSC075A12,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_HMSC062D05,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_KPL2003,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_KPL1847,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_HMSC067A01,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_HMSC065F07,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_HMSC078F01,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_sp_HMSC062D02
The relative abundance of those species is the relative abundance of the “main” species, look at this Unexpected output (format) - #2 by fbeghini for a brief explanation of what the additional species column means.
Relative abundance is calculated at the level of species, abundances of higher ranks are calculated by summing up the ranks below.
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Hmmmm thank you for the reply once again. Appreciate it!