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 |