Question: What does 'Coverage' in the total C/N/S cycles mean? about metabolic HOT 5 CLOSED

Hi, the coverage in this plot refers the sum of the average coverage of the MAGs (genome-level) (not of set of genes only genes) predicted to be involved in that process. For example, if there are 3 organisms involved in carbon oxidation, and from the mapping step it was inferred that Organisms A has 2% coverage, B has 5%, and C has 6% in the reads set you gave METABOLIC, then the "coverage value" for carbon oxidation would be 2+5+6 = 13%. You can think of coverage here as the relative "abundance" of the organisms compared to the "abundance" of all MAGS in that sample.

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Hi @susheelbhanu , yes you are correct that it does not mean that 45.1% of genomes have these genes. To know how many of your MAGS have that process, you would just take 583 MAGS divided by total number of MAGS in your original fasta folder.

Yes, you are correct BUT it is not the pathway that has that coverage, rather the MAGS that have the pathway. The coverage value would be out of a maximum of 100% -- since in my example above the 2%, 5% and 6% are already calculated as abundance out of the total number of reads (reads mapped divided by total number of reads X 100 = % value). You can interpret it (in your attached PDF) as: you have 583 MAGS that could potentially perform carbon oxidation, and that they correspond to 45.1% "relative abundance" in your sample.

from metabolic.

Yes. "num" here means the num of MAGs that have the function. "coverage" means the relative coverage of these MAGs within the total microbial community. They are different. The extreme condition would be that there is only one genome in 100 genomes to have this function, while, this genome has very high coverage (like, 95%). This situation could be interpreted as this genome is the major contributor to this function in the microbial community, unproportionally high to its genome num percentage in the microbial community.

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Thank you @patriciatran! So, this doesn't mean that 45.1% of the genomes have these set of genes, right?!

Rather out of a possible 100% coverage across all genomes, this pathway has 45% coverage?

Sorry for the redundant questions, but just trying to understand the implications of this value.

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Awesome, thank you very much for the detailed explanation.

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