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bedrock.bio

assembly_regions

Identifier

Section titled “Identifier”
refseq.assembly_regions

Description

Section titled “Description”

Genomic regions with alternate-scaffold and patch placements from assembly-specific *_assembly_regions.txt reports when NCBI supplies one.

Each row locates a named region on a chromosome and, when applicable, identifies the alternative or patch scaffold that covers it.

Assembly-unit accessions are parsed from the report’s Assembly-Units header and joined by unit_name.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.20'
    • 'GCF_000001635.27'
    • 'GCF_000002035.6'
    • 'GCF_000003025.6'

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 Partition column. Versioned RefSeq assembly accession (GCF accession).
unit_accession TEXT Versioned RefSeq assembly-unit accession from the report header, if the row is associated with an assembly unit.
genbank_unit_accession TEXT Versioned GenBank assembly-unit accession from the report header, if the row is associated with an assembly unit.
unit_name TEXT Assembly-unit name from the report, such as PATCHES or an ALT_REF_LOCI unit; null when not applicable.
region_name TEXT NCBI name of the chromosome region; it may recur for placements on multiple scaffolds.
chromosome TEXT Chromosome on which NCBI locates the region.
chromosome_start INT 1-based inclusive start coordinate of the region on chromosome.
chromosome_end INT 1-based inclusive end coordinate of the region on chromosome.
scaffold_role TEXT NCBI role of the placed scaffold, such as alt-scaffold, fix-patch, novel-patch, or CEN.
genbank_sequence_accession TEXT Versioned GenBank accession of the placed scaffold, if supplied.
sequence_accession TEXT Versioned RefSeq accession of the placed scaffold, if supplied; joins refseq.assembly_sequences.sequence_accession.