Question regarding to taxonomy classification about checkm

[donovan-h-parks]

The tree_qa indicates the placement of your bin within CheckM's reference genome tree. It appears your bin/genomes is in the familiy f__Porphyromonadaceae. The qa output indicates information about the marker set that was used to evaluate your bin. In this case, it was a marker set outside the p__Bacteroidetes, but within the domain k__Bacteria. The results here may represent some issues with the taxonomic assignment of IMG's reference genomes. The qa command indicates that a domain level set was used, but that this set consisted of 434 genomes. There are 419 p__Bacteroidetes genomes in the CheckM reference genome tree so it appears your bin is essentially being assessed with a p__Bacteroidetes-specific set of markers. We are currently working on cleaning up the taxonomic assignment of reference genomes to help clarify situations like this. Note that UID2569 indicate a specific node in CheckM's reference tree. You can use the tree_qa command to generate a newick tree and look at exactly where your bin was placed and what genomes are below node UID2569.