alignments

Identifier

refseq.alignments

Description

Explicit RefSeq sequence-to-assembly alignment blocks from genomic GFF3 rows.

Rows sharing an alignment_id are blocks of the same alignment. sequence_accession, start, and end locate the block on the assembly; the target_* fields locate its mapped interval on the aligned sequence.

Partitions

• assembly_accession
  • 'GCF_000001405.25'
  • 'GCF_000001405.40'
  • 'GCF_000001635.20'
  • 'GCF_000001635.27'
  • 'GCF_000001895.5'
  • 'GCF_000002035.6'
  • 'GCF_000002285.3'
  • 'GCF_000003025.6'
  • 'GCF_000003625.3'
  • 'GCF_003339765.1'
  • 'GCF_012559485.2'
  • 'GCF_015227675.2'
  • 'GCF_036323735.1'
  • 'GCF_037993035.2'
  • 'GCF_049350105.2'
  • 'GCF_052040795.1'
  • 'GCF_054392235.1'
  • 'GCF_964237555.1'

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 alignment block is annotated; joins refseq.assembly_sequences.sequence_accession.
start	INT	1-based inclusive start coordinate of the alignment block on sequence_accession.
end	INT	1-based inclusive end coordinate of the alignment block on sequence_accession.
score	DOUBLE	GFF alignment score, if supplied; its definition varies by alignment type and source.
is_forward_strand	BOOLEAN	Whether the alignment block is on the forward strand of sequence_accession; null when unspecified.
alignment_id	TEXT	Local GFF3 ID of the alignment; shared by blocks of a multi-block alignment and not a stable identifier.
alignment_type	TEXT	Source GFF3 alignment type.
annotation_method	TEXT	NCBI GFF column-2 annotation method or source, if supplied.
target_accession	TEXT	Versioned accession of the aligned target sequence from the GFF Target attribute.
target_start	INT	1-based inclusive start coordinate of the block on target_accession.
target_end	INT	1-based inclusive end coordinate of the block on target_accession.
is_target_forward_strand	BOOLEAN	Whether the target interval is in forward orientation.
gap	TEXT	Exonerate CIGAR-like GFF Gap edit script describing indels in the alignment block, if supplied.
gap_count	INT	Number of gap openings in the whole alignment from GFF gap_count, if supplied.
identity_count	INT	Number of matching bases in the whole alignment from GFF num_ident, if supplied.
mismatch_count	INT	Number of mismatching bases in the whole alignment from GFF num_mismatch, if supplied.
target_coverage_fraction	FLOAT	Gapped target-sequence coverage from GFF pct_coverage, normalized from percent to a fraction from 0 through 1, if supplied.
gapped_identity_fraction	FLOAT	Standard gapped alignment identity from GFF pct_identity_gap, normalized from percent to a fraction from 0 through 1, if supplied.
gap_open_identity_fraction	FLOAT	Alignment identity from GFF pct_identity_gapopen_only, counting every gap as one mismatch, normalized from percent to a fraction from 0 through 1, if supplied.
ungapped_identity_fraction	FLOAT	Alignment identity from GFF pct_identity_ungap, excluding gaps, normalized from percent to a fraction from 0 through 1, if supplied.
rank	INT	Source rank of this alignment among alternatives, if supplied.
bit_score	DOUBLE	BLAST bit score from GFF bit_score, if supplied.
e_value	DOUBLE	BLAST expectation value from GFF e_value, if supplied.
is_curated_alignment	BOOLEAN	Whether GFF curated_alignment=1 marks the alignment as curated; null when the source does not supply the attribute.
not_for_annotation_code	Int8	Numeric GFF not_for_annotation status code, if supplied; values 1 and 2 are observed and its detailed semantics are not documented by NCBI.