| accession |
NCBI assembly accession with RS_/GB_ prefix |
| AF |
Alignment Fraction - proportion of genome that aligned |
| ANI |
Average Nucleotide Identity as percentage |
| ANI_circumscription_radius |
ANI threshold for species membership |
| checkm_completeness |
CheckM genome completeness estimate |
| checkm_contamination |
CheckM contamination estimate |
| class |
Class name with c__ prefix |
| COG_category |
COG functional category code(s) |
| contig_count |
Number of contigs in assembly |
| corrected_mean_completness |
Completeness after pangenome-based correction |
| Description |
Functional description from seed ortholog |
| domain |
Domain rank (d__Archaea or d__Bacteria) |
| EC |
EC enzyme numbers, comma-separated |
| eggNOG_OGs |
Hierarchical EggNOG ortholog groups from root to most specific |
| evalue |
E-value of seed ortholog match (lower = better match) |
| faa_file_path_nersc |
Absolute path to protein FASTA file at NERSC filesystem |
| family |
Family name with f__ prefix |
| fna_file_path_nersc |
Absolute path to nucleotide FASTA file at NERSC filesystem |
| gc_percentage |
GC content percentage |
| gene_cluster_id |
Unique cluster identifier |
| gene_id |
Composite gene identifier constructed from NCBI nucleotide accession and CDS ... |
| genome1_id |
First genome in pairwise comparison |
| genome2_id |
Second genome in pairwise comparison |
| genome_id |
Genome accession with source prefix and version |
| genome_size |
Total genome size in base pairs |
| genus |
Genus name with g__ prefix |
| GOs |
GO terms, comma-separated |
| gtdb_representative |
Whether this genome is the GTDB species representative |
| GTDB_species |
GTDB species name with s__ prefix |
| gtdb_species_clade_id |
Species clade ID combining species name and representative genome |
| GTDB_taxonomy |
Full GTDB lineage from domain to genus (species not repeated) |
| gtdb_taxonomy |
Full GTDB taxonomy string |
| gtdb_taxonomy_id |
Full GTDB taxonomy lineage string for this genome |
| is_auxiliary |
Present in some but not all genomes |
| is_core |
Present in all (or nearly all) genomes |
| is_singleton |
Present in only one genome |
| KEGG_ko |
KEGG Orthology IDs |
| KEGG_Pathway |
KEGG pathway IDs, comma-separated |
| likelihood |
Log-likelihood from PPanGGOLiN Bayesian partitioning model |
| mean_initial_completeness |
Mean CheckM completeness of input genomes before filtering |
| mean_intra_species_AF |
Mean alignment fraction - proportion of genome aligning in ANI calculations |
| mean_intra_species_ANI |
Mean pairwise ANI among all genomes |
| metabolic_category |
Category - amino acid (aa) or carbon source |
| min_intra_species_AF |
Minimum alignment fraction observed between any two genomes |
| min_intra_species_ANI |
Minimum pairwise ANI observed |
| ncbi_bioproject_accession_id |
NCBI BioProject accession |
| ncbi_biosample |
NCBI BioSample accession |
| ncbi_biosample_accession_id |
NCBI BioSample accession with sample metadata |
| ncbi_biosample_id |
NCBI BioSample accession linking to sample metadata including isolation sourc... |
| ncbi_organism_name |
NCBI organism name including strain |
| ncbi_taxid |
NCBI taxonomy ID |
| no_aux_genome |
Number of auxiliary (shell) gene clusters |
| no_clustered_genomes_filtered |
Genomes passing quality filters used in pangenome analysis |
| no_clustered_genomes_unfiltered |
Total genomes assigned to species before quality filtering |
| no_core |
Number of core gene clusters |
| no_gene_clusters |
Total gene clusters (core + auxiliary + singleton) |
| no_genomes |
Number of genomes in pangenome analysis |
| no_singleton_gene_clusters |
Number of singleton clusters |
| number_of_iterations |
PPanGGOLiN model training iterations (0 = converged early) |
| order |
Order name with o__ prefix |
| pathway |
Pathway/compound name |
| PFAMs |
PFAM domain annotations, comma-separated |
| phylum |
Phylum name with p__ prefix |
| Preferred_name |
Gene symbol when available, "-" if none |
| protein_count |
Number of predicted protein-coding genes |
| protocol_id |
Analysis protocol version identifier |
| query_name |
Gene ID - links to Gene |
| representative_genome_id |
Reference genome for this species |
| score |
Bit score of seed ortholog alignment |
| score_category |
Categorical assessment of pathway completeness |
| seed_ortholog |
Best matching seed ortholog from eggNOG database |
| species |
Species name with s__ prefix |
| total_sum_of_loglikelihood_ratios |
Model fit quality metric |