Genome Data

Metadata record for a Genome

Attributes

• _version_ (number)
• additional_metadata (array of case insensitive strings) - Curated or user-supplied clinical / experimental tags that don’t map to fixed columns; exposed as searchable facets. ["hospital location: ICU", "host_health_state: Carriage"]
• altitude (case insensitive string) - Elevation of collection site, with units if known; useful for ecological studies. "1500 m"
• antimicrobial_resistance (array of case insensitive strings) - Values such as Resistant, Susceptible, Intermediate for one or more drugs. ["Resistant: CIP", "Susceptible: AMP"] (bv-brc.org)
• antimicrobial_resistance_evidence (case insensitive string) - Indicates whether the AMR value comes from Phenotype, AMR Panel, or Comment. "Phenotype" (bv-brc.org)
• assembly_accession (string) - Stable accession assigned by NCBI to the submitted assembly. "GCF_000005845.2"
• assembly_method (case insensitive string) - Free-text record of assembler name + version; displayed in sequence-quality reports. "SPAdes v3.15.4"
• authors (case insensitive string) - Comma-delimited list from the associated genome paper or GenBank record. "Smith AJ, Lee B, Patel C"
• bioproject_accession (string) - Links genome to its umbrella project record. "PRJNA123456"
• biosample_accession (string) - Connects genome to detailed sample metadata in BioSample. "SAMN00123456"
• biovar (case insensitive string) - Sub-classification based on biochemical profile. "biovar Anthracis"
• body_sample_site (case insensitive string) - Broad host body location (e.g. nasopharynx). "Blood"
• body_sample_subsite (case insensitive string) - Finer-grained location within body_sample_site. "Left median cubital vein"
• cds (integer) - Count of protein-coding genes annotated in the genome. 5221
• cds_ratio (number) - CDS count divided by genome length (×1000); proxy for gene density. 0.9
• cell_shape (case insensitive string) - Terms like coccus, rod, spirillum; supports phenotype filters. "rod"
• cgmlst_hc0 (string) - pHierCC cluster ID at HC0 (zero allele differences allowed); at this level almost every genome is unique.
• cgmlst_hc10 (string) - pHierCC cluster ID at HC10 (up to 10 allele differences allowed).
• cgmlst_hc100 (string) - pHierCC cluster ID at HC100 (up to 100 allele differences allowed); the broadest retained clustering level.
• cgmlst_hc2 (string) - pHierCC cluster ID at HC2 (up to 2 allele differences allowed); genomes in the same cluster differ by at most 2 assigned loci.
• cgmlst_hc20 (string) - pHierCC cluster ID at HC20 (up to 20 allele differences allowed).
• cgmlst_hc5 (string) - pHierCC cluster ID at HC5 (up to 5 allele differences allowed).
• cgmlst_hc50 (string) - pHierCC cluster ID at HC50 (up to 50 allele differences allowed).
• cgmlst_id (string) - Identifier linking the genome to its cgMLST typing record in the genome_typing collection.
• checkm_completeness (number) - Marker-gene based completeness estimate for MAGs / draft genomes. 98.7
• checkm_contamination (number) - Estimated contamination level from CheckM. 1.1
• chromosomes (integer) - Count of primary replicons labelled “chromosome”. 1
• city (case insensitive string) - Part of geographic metadata hierarchy. "Chicago"
• clade (string) - Used mainly for viral lineages (e.g. A(H1N1)pdm09). "Clade 7.2"
• class (case insensitive string) - From NCBI lineage. "Gammaproteobacteria"
• coarse_consistency (number) - Large-scale annotation consistency metric (0 – 100). 95.4
• collection_date (string) - Raw text from metadata; may include ranges or partial dates. "2019-05-17"
• collection_year (integer) - Extracted 4-digit year for faster faceting. 2019
• comments (array of case insensitive strings) - Additional remarks not captured in structured fields. ["possible lab contaminant"]
• common_name (string) - Informal or host-focused names. "E. coli O157:H7"
• completion_date (date) - When sequencing / assembly was declared finished. "2020-02-11T00:00:00Z"
• contig_l50 (integer) - Number of contigs whose summed length equals ≥50 % of genome. 22
• contig_n50 (integer) - Length of the shortest contig in the top 50 % by size. 245 876
• contigs (integer) - All sequence entries in the assembly. 131
• core_families (integer) - Number of pan-genome protein families present in ≥95 % of a genus; helps gauge essential gene set coverage. 1235
• core_family_ratio (number) - core_families divided by total PGFams for this genome. 0.86
• county (case insensitive string) - Mid-level geographic tag for U.S. / UK style addresses. "DuPage County"
• culture_collection (case insensitive string) - Depository and strain number (e.g. ATCC 25922). "ATCC 25922"
• date_inserted (date) - When the genome row entered BV-BRC. "2023-04-18T12:41:02Z"
• date_modified (date) - Updates whenever any field changes. "2025-05-01T08:17:33Z"
• depth (case insensitive string) - Environmental depth (soil core, water column) with units. "150 m below sea level"
• disease (array of case insensitive strings) - Pathologies linked to the organism. ["Tuberculosis"]
• family (case insensitive string) - From NCBI lineage. "Enterobacteriaceae"
• fine_consistency (number) - Detailed annotation consistency metric (0 – 100). 97.8
• gc_content (number) - (G + C) / total bases × 100. 50.8
• genbank_accessions (case insensitive string) - Comma-delimited GenBank accessions for all replicons. "CP000012, CP000013"
• genome_id * (string) - Stable BV-BRC identifier taxon.version. "511145.183"
• genome_length (integer) - Sum of all contig lengths. 5 403 617
• genome_name (case insensitive string) - Primary display name used in tables and downloads. "Escherichia coli K-12 MG1655"
• genome_quality (string) - One of Finished, High Quality Draft, Low Quality Draft, Metagenome Metagenome-Assembled Genome, etc. "Finished"
• genome_quality_flags (array of strings) - Specific issues (e.g. low_N50, possible_contamination). ["low_N50"]
• genome_status (case insensitive string) - Values such as Complete, Draft, WGS. "Complete"
• genus (case insensitive string) - From NCBI lineage. "Escherichia"
• geographic_group (case insensitive string) - Broad area bucket (e.g. Sub-Saharan Africa). "North America"
• geographic_location (case insensitive string) - Often “Country:Region” or GPS string. "USA: Illinois"
• gram_stain (case insensitive string) - Gram-positive, Gram-negative, or variable. "Gram-negative"
• h1_clade_global (array of strings) - One or more WHO/Nextstrain H1 global clade designations derived from the HA segment phylogeny. ["5.2a", "6B.1A"]
• h1_clade_us (array of strings) - USDA/IRMA H1 clade labels used for North-American swine surveillance. ["1A.3.3.2"]
• h3_clade (array of strings) - Nextstrain/WHO clades for H3 influenza viruses. ["3C.2a1b.2a.2"]
• h5_clade (array of strings) - WHO/OIE/FAO H5 nomenclature (e.g. 2.3.4.4b). ["2.3.4.4b"]
• h_type (integer) - Hemagglutinin subtype Hn (1 – 18); null for non-IAV genomes. 5
• habitat (case insensitive string) - Broad environment where the organism lives (e.g. marine, soil, host-associated). "freshwater sediment"
• host_age (case insensitive string) - Age or age-range text pulled from BioSample (units vary). "5 years"
• host_common_name (case insensitive string) - Vernacular host species name. "Mallard duck"
• host_gender (case insensitive string) - Male, Female, Unknown. "Female"
• host_group (case insensitive string) - Broad host class (human, avian, swine, equine, other mammal). "avian"
• host_health (case insensitive string) - Free-text descriptor (Healthy, Diseased, Deceased, etc.). "Symptomatic"
• host_name (case insensitive string) - Raw text as provided by submitter; may mix name & strain. "Broiler chicken"
• host_scientific_name (case insensitive string) - NCBI-taxon scientific name; enables taxonomic lookup. "Anas platyrhynchos"
• hypothetical_cds (integer) - Number of protein-coding genes without functional annotation. 1 237
• hypothetical_cds_ratio (number) - hypothetical_cds / cds; quality-of-annotation metric. 0.24
• isolation_comments (case insensitive string) - Curator or submitter comments about sampling context. "Isolated during LPAI surveillance on live-bird market"
• isolation_country (case insensitive string) - ISO-recognized country string. "USA"
• isolation_site (case insensitive string) - Specific facility, farm, ward, etc. "DuPage County Animal Shelter"
• isolation_source (case insensitive string) - Text such as nasal swab, feces, soil, water. "Cloacal swab"
• kingdom (case insensitive string) - Derived from NCBI lineage; e.g. Bacteria, Viruses, Fungi. "Viruses"
• lab_host (case insensitive string) - Cell line or animal used for passage. "MDCK cells"
• latitude (case insensitive string) - Signed decimal ° or DMS string. "41.7886"
• lineage (string) - Concise lineage string (B.1.1.7, 1/2a, etc.) or genotypic set for bacteria. "clonal complex 11"
• longitude (case insensitive string) - Signed decimal ° or DMS string. "-88.1620"
• mat_peptide (integer) - Number of translated mature peptides (mainly viruses). 11
• missing_core_family_ids (array of strings) - List of expected core families missing from the genome; aids MAG completeness review. ["PGF_04251777"]
• mlst (case insensitive string) - Multi-Locus Sequence Typing result (scheme-specific). "ST11 (Achtman scheme)"
• motility (case insensitive string) - Motile, Non-motile, Gliding, etc. "Motile"
• n_type (integer) - Neuraminidase subtype Nn (1 – 11) for influenza. 1
• ncbi_project_id (string) - Historical project identifier (now superseded by BioProject). "180"
• nearest_genomes (array of strings) - List of BV-BRC genome_ids within the “Similar Genome Finder” threshold. ["511145.183", "511145.184"]
• optimal_temperature (case insensitive string) - Text or numeric range (°C) for culture growth. "37 °C"
• order (case insensitive string) - From NCBI lineage. "Enterobacterales"
• organism_name (case insensitive string) - Extra strain designations or submitter-preferred name. "Salmonella enterica Typhimurium 14028s"
• other_clinical (array of case insensitive strings) - Flexible list of keywords (e.g. antibiotic use, ICU patient). ["ICU patient"]
• other_environmental (array of case insensitive strings) - Describes abiotic factors like pH, heavy-metal load. ["pH 3.5", "anaerobic digester"]
• other_names (array of case insensitive strings) - Helps fuzzy search on old nomenclature. ["EHEC O157:H7"]
• other_typing (array of case insensitive strings) - PFGE, serogroup, biochemical panel outcomes. ["PFGE: XbaI pattern 26"]
• outgroup_genomes (array of strings) - Reference genomes used as outgroup in comparative trees. ["511145.6"]
• owner (string) - BV-BRC user or organization that controls the record. "CDC-Flu-Lab"
• oxygen_requirement (case insensitive string) - Aerobic, Facultative, Anaerobic, Microaerophilic. "Aerobic"
• p2_genome_id (integer) - Numeric genome ID from the retired PATRIC2 system; retained for cross-walks. 83332
• partial_cds (integer) - Number of coding sequences flagged as partial. 87
• partial_cds_ratio (number) - partial_cds / cds; assembly/annotation quality signal. 0.016
• passage (case insensitive string) - Text like E3/M1 (egg / MDCK passage) or original. "1× MDCK passage"
• pathovar (case insensitive string) - Intra-species pathogenic variety (mainly Pseudomonas/Xanthomonas). "pv. oryzae"
• patric_cds (integer) - Protein-coding genes predicted by the RASTtk pipeline. 5 211
• ph1n1_like (string) - “yes” if HA derives from 2009 pandemic lineage. "yes"
• phenotype (array of case insensitive strings) - Broad phenotypic descriptors (acid-tolerant, spore-former). ["spore-former"]
• phylum (case insensitive string) - From NCBI lineage. "Proteobacteria"
• plasmids (integer) - Number of replicons flagged as plasmids. 3
• plfam_cds (integer) - Gene count mapped to a PATRIC local family. 4 873
• plfam_cds_ratio (number) - plfam_cds / cds; annotation coverage metric. 0.935
• public (boolean) - true if the genome is publicly viewable; false for private workspaces. True
• publication (string) - PubMed ID or full citation for reference genome. "PMID:23212345"
• reference_genome (string) - "Reference" or empty; used in analysis defaults. "Reference"
• refseq_accessions (case insensitive string) - Comma-separated RefSeq replicon IDs. "NC_000913.3, NC_007779.1"
• refseq_cds (integer) - Protein-coding gene count from NCBI annotation. 4 289
• refseq_project_id (string) - Identifier of the RefSeq genome project. "GCF_000005845"
• rrna (integer) - Total 5S + 16S + 23S copies. 22
• salinity (case insensitive string) - Text or numeric range (% or ppt). "3 % NaCl"
• season (string) - Year/season string; common in influenza metadata. "2023-2024"
• segment (array of strings) - For segmented viruses (PB2, HA, NA, etc.). "HA"
• segments (integer) - Genome segment count (Influenza = 8). 8
• sequencing_centers (case insensitive string) - Free-text list of institutions that produced the reads. "Illumina BaseSpace, CDC"
• sequencing_depth (case insensitive string) - “×” value or range, often with platform. "120×"
• sequencing_platform (case insensitive string) - Illumina MiSeq, Oxford Nanopore MinION, etc. "Illumina NextSeq 2000"
• sequencing_status (case insensitive string) - Complete, Draft, 1st pass, etc. "Draft"
• serovar (case insensitive string) - O/H serotypes or Salmonella serovars. "Typhimurium"
• species (case insensitive string) - From NCBI; case-insensitive for search. "Escherichia coli"
• sporulation (case insensitive string) - Spore-forming / Non-spore-forming. "Non-spore-forming"
• sra_accession (string) - Raw-read accession at NCBI SRA. "SRR12345678"
• state_province (case insensitive string) - Sub-country administrative region. "Illinois"
• strain (case insensitive string) - Canonical strain/ isolate label. "K-12 MG1655"
• subclade (string) - Finer subdivision below clade (often influenza). `"2.3.4.4b-2"``
• subtype (string) - Influenza HxNy or other virus subtype text. "H5N1"
• superkingdom (case insensitive string) - Archaea, Bacteria, Eukaryota, Viruses. "Bacteria"
• taxon_id (integer) - Numerical taxon identifier. 562
• taxon_lineage_ids (array of strings) - Array of ancestor taxon IDs up to root. ["2","1224","1236","91347","543"]
• taxon_lineage_names (array of strings) - Array parallel to taxon_lineage_ids. ["Bacteria","Proteobacteria","Gammaproteobacteria","Enterobacterales","Enterobacteriaceae"]
• temperature_range (case insensitive string) - Psychrophile, Mesophile, Thermophile or explicit °C range. "Mesophile"
• trna (integer) - Number of predicted tRNA genes. 88
• type_strain (case insensitive string) - “yes” if the isolate is the species type-strain. "yes"
• user_read (array of strings) - BV-BRC user/org UUIDs permitted to view the record. ["public"]
• user_write (array of strings) - User/org UUIDs with edit rights. ["[email protected]"]

API

https://www.bv-brc.org/api/genome/1313.5458