Data dictionary - Ecogenomics/GTDBNCBI GitHub Wiki
The fields in the GTDB ARB file are as follows:
| Name | Description | Example |
|---|---|---|
| accession | Unique genome identifier indicating the genome source (RS = RefSeq; GB = GenBank) and NCBI accession number | RS_GCF_000009045.1 |
| aligned_seq | Alignment of the bac120 or ar53 amino acid marker genes | GRR...E |
| ambiguous_bases | Number of ambiguous bases in genome assembly | 0 |
| checkm2_completeness | Estimated completeness of genome using CheckM v2 | 100 |
| checkm2_contamination | Estimated contamination of genome using CheckM v2 | 0.05 |
| checkm2_model | Model used by CheckM v2 to estimate completeness and contamination | Specific |
| checkm_completeness | Estimated completeness of genome using CheckM v1 | 99.81 |
| checkm_contamination | Estimated contamination of genome using CheckM v1 | 0.25 |
| checkm_genome_count | Number of reference genomes used by CheckM v1 for quality estimation | 36 |
| checkm_marker_count | Number of marker genes used by CheckM v1 to estimate genome quality | 1200 |
| checkm_marker_lineage | Lineage of marker genes used by CheckM v1 to estimate genome quality | g__Bacillus (UID865) |
| checkm_marker_set_count | Number of marker sets used by CheckM v1 to estimate genome quality | 269 |
| checkm_strain_heterogeneity | Estimated strain heterogeneity of genome using CheckM v1 | 0 |
| checkm_strain_heterogeneity_100 | Estimated strain heterogeneity when only considering 100% identical marker genes | 0 |
| coding_bases | Number of coding bases in genome | 3705237 |
| coding_density | Coding density of genome | 87.89 |
| contig_count | Number of contigs in genome assembly | 1 |
| db_name | Canonical genome ID used by ARB; must match leaf node ID in Newick tree | G000009045 |
| description | Always blank; required by ARB? | |
| dsmz_type_designation | Type strain designation as recognized by the DSMZ culture collection | type strain of species |
| formatted_accession | Canonical genome ID; SHOULD BE REMOVED | G000009045 |
| gc_count | Number of GC bases in genome | 1834396 |
| gc_percentage | Percent GC-content of genome | 43.51 |
| genome_size | Size of genome in base pairs | 4215606 |
| gtdb_class | Class classification according to GTDB taxonomy | c__Bacilli |
| gtdb_cluster_ncbi_species | Summary counts of NCBI species names observed within this GTDB cluster | s__Bacillus subtilis: 1155... |
| gtdb_cluster_size | Mumber of genomes in this GTDB species cluster | 1249 |
| gtdb_clustered_genomes | List of genome IDs contained in GTDB cluster | G024259785;G017753785... |
| gtdb_domain | Domain classification according to GTDB taxonomy | d__Bacteria |
| gtdb_family | Family classification according to GTDB taxonomy | f__Bacillaceae |
| gtdb_genome_representative | ID of representative genome of the GTDB species cluster to which this genome is assigned | RS_GCF_000009045.1 |
| gtdb_genus | Genus classification according to GTDB taxonomy | g__Bacillus |
| gtdb_genus_type_species | Flag indicating if the genome represents the type species for the assigned GTDB genus | True |
| gtdb_order | Order classification according to GTDB taxonomy | o__Bacillales |
| gtdb_phylum | Phylum classification according to GTDB taxonomy | p__Bacillota |
| gtdb_representative | Indicates if this genome is the representative of a GTDB species cluster | True |
| gtdb_species | Species classification according to GTDB taxonomy | s__Bacillus subtilis |
| gtdb_species_type_strain | Flag indicating if the genome represents the type strain for the assigned GTDB species ??? - does a type strain designation depend on the assigned species name ??? | True |
| gtdb_taxonomy | Full GTDB taxonomy string | d__Bacteria;p__Bacillota... |
| gtdb_type_designation_ncbi_taxa | Indicates if genome is assembled from the type strain of a species or subspecies according to its NCBI classification - ??? does this actually depend on species assignment or just the strain ID ??? | type strain of species |
| gtdb_type_designation_ncbi_taxa_sources | Authoritative nomenclatural sources supporting type designation in gtdb_type_designation_ncbi_taxa | LPSN |
| gtdb_type_species_of_genus | Indicates if genome is assembled from the type species of the genus - ??? is this for the NCBI species classification; does this account for LPSN and SeqCode ??? | True |
| l50_contigs | L50 of contigs in genome assembly | 1 |
| l50_scaffolds | L50 of scaffolds in genome assembly | 1 |
| longest_contig | Longest contig in genome assembly | 4215606 |
| longest_scaffold | Longest scaffold in genome assembly | 4215606 |
| lpsn_priority_year | Nomenclatural priority year for the taxon recorded in LPSN | 1835 |
| lpsn_type_designation | Specific type strain designation defined in LPSN - ??? this description seems incomplete as this must require matching of type strains between NCBI and LPSN to draw such conclusions for a specific genome ??? | type strain of species |
| lsu_23s_contig_len | Length of contig containing selected representative 23S rRNA gene | 4215606 |
| lsu_23s_count | Number of 23S rRNA genes in genomes | 10 |
| lsu_23s_length | Length of selected representative 23S rRNA gene | 2924 |
| lsu_23s_query_id | Identifier of contig containing selected representative 23S rRNA gene | NC_000964.3 |
| lsu_5s_contig_len | Length of contig containing selected representative 5S rRNA gene | 4215606 |
| lsu_5s_count | Number of 5S rRNA genes in genomes | 10 |
| lsu_5s_length | Length of selected representative 5S rRNA gene | 111 |
| lsu_5s_query_id | Identifier of contig containing selected representative 5S rRNA gene | NC_000964.3 |
| lsu_silva_23s_blast_align_len | BLAST alignment length of top hit between representative 23S gene and SILVA LSU DB | 2924 |
| lsu_silva_23s_blast_bitscore | BLAST bitscore of top hit between representative 23S gene and SILVA LSU DB | 5400 |
| lsu_silva_23s_blast_evalue | BLAST e-value of top hit between representative 23S gene and SILVA LSU DB | 0 |
| lsu_silva_23s_blast_perc_identity | BLAST percent identity of top hit between representative 23S gene and SILVA LSU DB | 100 |
| lsu_silva_23s_blast_subject_id | SILVA identifier of top hit between representative 23S gene and SILVA LSU DB | D84213.7327.10254 |
| lsu_silva_23s_taxonomy | SILVA taxonomy of top hit between 23S genes and SILVA LSU DB | Bacteria;Bacillota... |
| mean_contig_length | Average length of contigs in genome assembly | 4215606 |
| mean_scaffold_length | Average length of scaffolds in genome assembly | 4215606 |
| mimag_high_quality | Indicates if genome meets the high-quality MIMAG criteria | True |
| mimag_low_quality | Indicates if genome meets the low-quality MIMAG criteria | False |
| mimag_medium_quality | Indicates if genome meets the medium-quality MIMAG criteria | False |
| msa_aa_count | Total count of amino acids in the bac120 or ar53 multiple sequence alignment | 39736 |
| msa_gene_count | Number of bac120 or ar53 marker genes identified in genome | 119 |
| msa_length | Number of aligned columns in bac120 or ar53 multiple sequence alignment | 41084 |
| msa_num_marker_genes | Number of identified bac120 or ar53 marker genes | 120 |
| multiple_homologs | Number of bac120 or ar53 marker genes detected multiple times in genome assembly | 1 |
| n50_contigs | N50 of contigs in genome assembly | 4215606 |
| n50_scaffolds | N50 of scaffolds in genome assembly | 4215606 |
| ncbi_asm_name | Name of the assembly provided by the submitter to NCBI | ASM904v1 |
| ncbi_assembly_level | NCBI assembly level: Complete Genome, Chromosome, Scaffold, Contig | Complete Genome |
| ncbi_assembly_name | NCBI assembly name | ASM904v1 |
| ncbi_assembly_type | NCBI assembly type | na |
| ncbi_bioproject | NCBI BioProject ID for genome | PRJNA76 |
| ncbi_biosample | NCBI BioSample ID for genome | SAMEA3138188 |
| ncbi_cds_count | Total count of coding sequences (CDS) defined in the NCBI record | 4240 |
| ncbi_contig_count | Number of contigs in genome according to NCBI | None |
| ncbi_contig_n50 | N50 of contigs in genome according to NCBI | None |
| ncbi_country | Country associated with genome assembly at NCBI | None |
| ncbi_date | Date genomes was submitted to NCBI | 2009-08-12 |
| ncbi_excluded_from_refseq | Notes or reasons if the genome was excluded from the NCBI RefSeq database | None |
| ncbi_gbrs_paired_asm | Accession number for the corresponding paired NCBI GenBank/RefSeq assembly ID. | GCA_000009045.1 |
| ncbi_genbank_assembly_accession | NCBI GenBank assembly accession. | GCA_000009045.1 |
| ncbi_genome_category | NCBI genome category indicating if genomes was assembled from a single cell or metagenome. If none, the assumption is that it is an isolate genome. | None |
| ncbi_genome_representation | Indicates by NCBI if genome is full or partial | full |
| ncbi_genus | Genus classification according to NCBI taxonomy | g__Bacillus |
| ncbi_isolate | Isolate name at NCBI | na |
| ncbi_isolation_source | Isolation source at NCBI | None |
| ncbi_lat_lon | Latitude and longitude associated with genome assembly at NCBI | None |
| ncbi_molecule_count | Molecule count at NCBI | 1 |
| ncbi_ncrna_count | Non-coding RNA count at NCBI | 0 |
| ncbi_not_used_as_type | NCBI flag determining if the genome assembly was explicitly excluded from being used as a type material. | False |
| ncbi_organism_name | Organism name at NCBI | Bacillus subtilis subsp. subtilis str. 168 |
| ncbi_paired_asm_comp | Comparison status detailing how this assembly relates to its paired NCBI GenBank/RefSeq counterpart | identical |
| ncbi_protein_count | Protein count at NCBI | 4177 |
| ncbi_refseq_assembly_and_genbank_assemblies_identical | Indicates whether the NCBI RefSeq and GenBank assembly records are exactly identical | yes |
| ncbi_refseq_category | NCBI RefSeq genome category | reference genome |
| ncbi_region_count | Count of specific annotated sequence regions identified by NCBI | None |
| ncbi_release_type | Defines whether the NCBI sequence release is a major or minor update | major |
| ncbi_rrna_count | rRNA count at NCBI | 30 |
| ncbi_scaffold_count | Number of scaffolds at NCBI | 1 |
| ncbi_scaffold_l50 | L50 of scaffolds according to NCBI | 1 |
| ncbi_scaffold_n50 | N50 of scaffolds according to NCBI | 4215606 |
| ncbi_scaffold_n75 | N75 of scaffolds according to NCBI | 4215606 |
| ncbi_scaffold_n90 | N90 of scaffolds according to NCBI | 4215606 |
| ncbi_seq_rel_date | NCBI sequence release date | 2009-08-12 |
| ncbi_spanned_gaps | Number of spanned gaps according to NCBI | 0 |
| ncbi_species | Species classification according to NCBI taxonomy | s__Bacillus subtilis |
| ncbi_species_taxid | NCBI species taxonomy identifier | 1423 |
| ncbi_ssu_count | Number of 16S rRNA genes in genome according to NCBI | 0 |
| ncbi_strain_identifiers | NCBI strain information from the assembly report. | 168 |
| ncbi_submitter | Submitter at NCBI | BSNR |
| ncbi_taxid | NCBI taxonomy identifier | 224308 |
| ncbi_taxonomy | Standardized NCBI taxonomy string | d__Bacteria;p__Bacillota... |
| ncbi_taxonomy_unfiltered | Full NCBI taxonomy string, including non-standard or unspecified ranks | d__Bacteria;x__Bacillati... |
| ncbi_top_level_count | Count of top-level genomic sequences in the NCBI assembly | 1 |
| ncbi_total_gap_length | Length of all gaps in genome according to NCBI | 0 |
| ncbi_total_length | Size of genome in base pairs according to NCBI | 4215606 |
| ncbi_translation_table | Translation table of genome according to NCBI | 11 |
| ncbi_trna_count | tRNA count for genome according to NCBI | 86 |
| ncbi_type_material_designation | Indicates if genome is assembled from type material according to NCBI | assembly from type material |
| ncbi_ungapped_length | Number of ungapped bases according to NCBI | 4215606 |
| ncbi_unspanned_gaps | Number of unspanned gaps according to NCBI | 0 |
| ncbi_version_status | Status of the NCBI assembly version (e.g., latest, replaced) | latest |
| ncbi_wgs_formatted | Formatted version of the NCBI WGS prefix/accession | None |
| ncbi_wgs_master | NCBI WGS accession | na |
| organism_name | The full scientific name of the organism at NCBI, including subspecies and strain where applicable | Bacillus subtilis subsp. subtilis str. 168 |
| protein_count | Number of proteins predicted for genome assembly | 4226 |
| scaffold_count | Number of scaffolds in genome assembly | 1 |
| seqcode_class_status | Status of the class-level name validation in SeqCode | None |
| seqcode_classification | Full taxonomic classification recognized by SeqCode | None |
| seqcode_created_at | Date when the SeqCode record was created | None |
| seqcode_family_status | Status of the family-level name validation in SeqCode | None |
| seqcode_genus_status | Status of the genus-level name validation in SeqCode | None |
| seqcode_id | Unique identifier assigned to the organism within the SeqCode registry | None |
| seqcode_name | Proposed or accepted taxonomic name in the SeqCode registry | None |
| seqcode_order_status | Status of the order-level name validation in SeqCode | None |
| seqcode_phylum_status | Status of the phylum-level name validation in SeqCode | None |
| seqcode_priority_date | The nomenclatural priority date recognized by SeqCode | None |
| seqcode_proposed_by | Author or group who proposed the SeqCode taxonomic name | None |
| seqcode_rank | Taxonomic rank assigned by the SeqCode registry | None |
| seqcode_species_status | Status of the species-level name validation in SeqCode | None |
| seqcode_type_genus_of_class | Flag indicating if this is the type genus for the class under SeqCode rules | None |
| seqcode_type_genus_of_family | Flag indicating if this is the type genus for the family under SeqCode rules | None |
| seqcode_type_genus_of_order | Flag indicating if this is the type genus for the order under SeqCode rules | None |
| seqcode_type_genus_of_phylum | Flag indicating if this is the type genus for the phylum under SeqCode rules | None |
| seqcode_type_species_of_genus | Flag indicating if this is the type species for the genus under SeqCode rules | None |
| seqcode_updated_at | Date when the SeqCode record was last modified | None |
| seqcode_url | Direct link to the organism's nomenclature record in the SeqCode registry | None |
| ssu_contig_len | Length of contig containing selected representative 16S rRNA gene | 4215606 |
| ssu_count | Number of 16S rRNA genes in genome assembly | 10 |
| ssu_gg_blast_align_len | BLAST alignment length of top hit between representative 16S gene and Greengenes DB | None |
| ssu_gg_blast_bitscore | BLAST bitscore of top hit between representative 16S gene and Greengenes DB | None |
| ssu_gg_blast_evalue | BLAST e-value of top hit between representative 16S gene and Greengenes DB | None |
| ssu_gg_blast_perc_identity | BLAST percent identity of top hit between representative 16S gene and Greengenes DB | None |
| ssu_gg_blast_subject_id | Greengenes ID of top BLAST hit between representative 16S gene and Greengenes DB | None |
| ssu_gg_length | Length of the representative 16S gene queried against the Greengenes DB | None |
| ssu_gg_query_id | Identifier of the representative 16S gene queried against the Greengenes DB | None |
| ssu_gg_taxonomy | Greengenes taxonomy of top hit between representative 16S gene and Greengenes DB | None |
| ssu_length | Length of representative 16S rRNA gene selected from genome | 1548 |
| ssu_query_id | Identifier of contig containing representative 16S rRNA gene | NC_000964.3 |
| ssu_silva_blast_align_len | BLAST alignment length of top hit between representative 16S gene and SILVA SSU DB | 1548 |
| ssu_silva_blast_bitscore | BLAST bitscore of top hit between representative 16S gene and SILVA SSU DB | 2859 |
| ssu_silva_blast_evalue | BLAST e-value of top hit between representative 16S gene and SILVA SSU DB | 0 |
| ssu_silva_blast_perc_identity | BLAST percent identity of top hit between representative 16S gene and SILVA SSU DB | 100 |
| ssu_silva_blast_subject_id | SILVA ID of of top hit between representative 16S gene and SILVA SSU DB | CP011115.166498.168052 |
| ssu_silva_taxonomy | SILVA taxonomy of top hit between representative 16S gene and SILVA SSU DB | Bacteria;Bacillota... |
| total_gap_length | Length of all gaps in genome assembly | 0 |
| trna_aa_count | Number of standard amino acids with a tRNA in genome assembly | 19 |
| trna_count | Total number of identified tRNAs in genome assembly | 86 |
| trna_selenocysteine_count | Number of tRNAs for selenocysteine in genome assembly | 0 |
| username | Legacy field; SHOULD BE REMOVED | None |