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bedrock.bio

sequence_annotations

Identifier

Section titled “Identifier”
refseq.sequence_annotations

Description

Section titled “Description”

RefSeq sequence-level annotations from explicit genomic GFF3 rows. annotation_type preserves the source type; the table name avoids ambiguity with the literal sequence_feature source type.

A source ID can label multiple intervals.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001215.4'
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.20'
    • 'GCF_000001635.27'
    • 'GCF_000002035.6'
    • 'GCF_000002985.6'
    • 'GCF_000003625.3'
    • 'GCF_000005845.2'
    • 'GCF_000146045.2'

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).
sequence_accession TEXT Versioned RefSeq nucleotide sequence accession on which the annotation is located; joins refseq.assembly_sequences.sequence_accession.
start INT 1-based inclusive start coordinate of the annotated interval.
end INT 1-based inclusive end coordinate of the annotated interval.
is_forward_strand BOOLEAN Whether the annotated interval is on the forward strand; null when the GFF strand is unspecified.
sequence_annotation_id TEXT Local GFF3 ID of the annotation; not a stable RefSeq identifier and can recur across intervals.
annotation_type TEXT Source GFF3 sequence-annotation feature type.
annotation_method TEXT NCBI GFF column-2 annotation method or source, if supplied.
db_xrefs STRUCT(db TEXT, id TEXT)[] Database cross-references from GFF Dbxref; each item has a database and identifier, which may contain colons.
annotation_name TEXT Annotation name from GFF standard_name, if supplied.
associated_gene_symbol TEXT Gene symbol from GFF gene, if supplied; this is not a local GFF gene-ID join.
allele_name TEXT Allele name from GFF allele, if supplied.
is_pseudogene BOOLEAN Whether GFF pseudo=true marks the annotation as pseudogenic.
function TEXT Free-text functional description from GFF function, if supplied.
experiments TEXT[] Percent-decoded experimental-evidence entries from the comma-separated GFF experiment attribute.
is_partial BOOLEAN Whether NCBI marks the annotation as partial with GFF partial=true.
is_start_partial BOOLEAN Whether NCBI marks the column-4 start boundary as partial with GFF start_range.
is_end_partial BOOLEAN Whether NCBI marks the column-5 end boundary as partial with GFF end_range.
note TEXT Free-text GFF Note annotation, if supplied.