Data dictionary

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