The first block describes general information: Gram, NCBI tax ID and taxonomy, total number of CDS and length.
The second block presents the taxonomic classification according to GTDBtk.
The third block presents the completness and contamination as estimated by CheckM.
The following tables give some information about the replicons of the genome such as: Length, GC%, Ribosomal RNAs, tRNAs types, Annotations Status, Average CDS length, Repeated regions, Average intergenic length, Protein coding density, number of contigs/scaffolds etc.
eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. An Orthologous Group (OG) is defined as a cluster of three or more homologous sequences that diverge from the same speciation event. COG functional categories are updated for each OG.eggNOG-mapper is used to transfer functional information from precomputed Orthologous Groups (OGs) from the EggNOG database to novel sequences.
To find the homologs, the tool analyses the similarity results between the genes of each organism and the set of 206 genes from 7 genomes (Escherichia coli K12, Bacillus subtilis 168, Candidatus Blochmania floridanus, Buchnera aphidicola APS, Buchnera aphidicola Bp, Buchnera aphidicola Sg and Mycoplasma genitalium G37).
The candidate genes have to fill one of the 2 following conditions :
- share a BBH relationship with a minLRap > 0.5
- belong to a synteny group