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Table 1 Abundance metrics included in SQMtools and their interpretation in the full metagenome and in taxonomic and functional subsets

From: SQMtools: automated processing and visual analysis of ’omics data with R and anvi’o

 

Functions / Taxonomy

Functions

Taxonomy

 

Scaling method

Abund

TPM

Copy number

Percent

 

Calculation

Reads per function or taxon

106 × reads per kilobase of each function / total reads per kilobase of all functions

Coverage of function /

Coverage of RecA

100 × reads per taxon / Total reads

Full data

Interpretation in the full data

Reads from each function or taxon in the whole metagenome

Genes from each function per million genes in the whole metagenome

Average copies of each function per genome in the whole metagenome

Percentage of each taxonomic group in the whole metagenome

subsetTax/subsetBin

Rescaled in the new subset?

Not applicable

Yes, by taxonomy

Yes, by taxonomy

No

Interpretation in the subset

Reads from each function or taxon in the selected taxon or bin

Genes from each function per miIlion genes in the selected taxon or bin

Average copies of the function per genome from the selected taxon or bin

Percentage of each of the selected taxonomic groups in the whole metagenome

subsetFun

Rescaled in the new subset?

Not applicable

No

No

No

Interpretation in the subset

Reads from each function or taxon in the subset

Genes from each function in the subset per million genes in the metagenome

Average copies per genome of the functions in the subset per genome in the metagenome

Percentage of each taxonomic group in the whole metagenome, counting only the reads assigned to the functions in the subset