assembly_summary
Identifier
Section titled “Identifier”Description
Section titled “Description”Current and historical RefSeq genome assemblies from NCBI master summary files, one row per assembly.
assembly_name is NCBI’s human-readable asm_name label and may not be globally unique.
Use assembly_url to locate the assembly package’s annotation and sequence files.
Partitions
Section titled “Partitions”Not partitioned.
Schema
Section titled “Schema”| Column | Type | Description |
|---|---|---|
sources |
STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[] |
Original external inputs used to produce the row. Each item contains its source URL, filename, HTTP Last-Modified timestamp when available, and computed SHA-256 checksum. |
assembly_accession |
TEXT |
Versioned RefSeq assembly accession (GCF accession). |
bioproject_accession |
TEXT |
NCBI BioProject accession associated with the assembly, if supplied. |
biosample_accession |
TEXT |
NCBI BioSample accession associated with the assembly, if supplied. |
wgs_master_accession |
TEXT |
GenBank Nucleotide accession and version for the Whole Genome Shotgun project master record, if applicable. Complete-genome and clone-based assemblies do not have a WGS master record. |
is_historical |
BOOLEAN |
Whether this row originated from NCBI’s historical, rather than current, RefSeq assembly summary. |
version_status |
TEXT |
NCBI status of the assembly version, such as latest, replaced, suppressed, or withdrawn. |
refseq_exclusion_reason |
TEXT |
NCBI excluded_from_refseq reason for exclusion from RefSeq, if applicable. |
assembly_not_live_date |
DATE |
Date NCBI marked the assembly as no longer live, if applicable. |
is_reference |
BOOLEAN |
Whether NCBI designates the assembly as that species’ RefSeq reference genome. |
organism_taxon_id |
TEXT |
Opaque-string NCBI taxonomy ID assigned to the organism represented by this assembly; maps to registry.taxa.taxon_id. |
species_taxon_id |
TEXT |
Opaque-string NCBI taxonomy ID assigned to the assembly’s species; joins to Ensembl taxonomy_id. |
organism_name |
TEXT |
Scientific organism name reported by NCBI. |
infraspecific_names |
STRUCT(type TEXT, name TEXT)[] |
Infraspecific names reported by NCBI, parsed into type and name pairs, such as strain, breed, cultivar, or ecotype. |
isolate |
TEXT |
Isolate name reported by NCBI, if supplied. |
assembly_level |
TEXT |
NCBI-reported assembly completeness classification. |
release_type |
TEXT |
NCBI-reported release classification. |
genome_representation |
TEXT |
NCBI-reported extent of genome representation. |
sequence_release_date |
DATE |
Date the assembly sequence was released in an INSDC database (DDBJ, ENA, or GenBank). |
assembly_name |
TEXT |
NCBI asm_name: a human-recognizable assembly label, including its patch where applicable (for example, GRCh38.p14). |
assembly_submitter |
TEXT |
Organization or individual that submitted the assembly. |
genbank_assembly_accession |
TEXT |
Paired GenBank assembly accession (GCA accession with version), if NCBI provides one. |
is_identical_to_genbank |
BOOLEAN |
Whether NCBI reports the paired GenBank assembly as identical; null when no comparison is available. |
assembly_url |
TEXT |
NCBI directory URL for the RefSeq assembly package and its annotation and sequence files. |
relation_to_type_material |
TEXT |
NCBI-reported relationship of the organism to type material, if supplied. |
assembly_type |
TEXT |
Ploidy or assembly type reported by NCBI, if supplied. |
organism_group |
TEXT |
NCBI organism group, if supplied. |
assembly_size |
BIGINT |
Total assembly length in base pairs, if supplied. |
assembly_size_ungapped |
BIGINT |
Total ungapped assembly length in base pairs, if supplied. |
assembly_gc_fraction |
FLOAT |
Assembly GC content as a fraction from 0 through 1, if supplied. |
assembly_replicon_count |
INT |
Number of replicons in the assembly, if supplied. |
assembly_scaffold_count |
INT |
Number of scaffolds in the assembly, if supplied. |
assembly_contig_count |
INT |
Number of contigs in the assembly, if supplied. |
annotation_provider |
TEXT |
Organization that supplied the current annotation, if supplied. |
annotation_name |
TEXT |
NCBI annotation release name or version, if supplied. |
annotation_date |
DATE |
Date of the current annotation release, if supplied. |
total_gene_count |
INT |
Total annotated gene count, if supplied. |
protein_coding_gene_count |
INT |
Protein-coding annotated gene count, if supplied. |
non_coding_gene_count |
INT |
Non-coding annotated gene count, if supplied. |
pubmed_ids |
TEXT[] |
PubMed identifiers associated with the assembly. |