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bedrock.bio

refseq.sequence_alterations

import bedrock_bio as bb

rel = bb.load_table('refseq.sequence_alterations')
rel = rel.filter("assembly_accession = 'GCF_000001405.25'")

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources assembly_accession sequence_accession start end is_forward_strand sequence_alteration_id alteration_type annotation_method db_xrefs function experiments note
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 236202705 236202705 <NA> id-GeneID:107546745-7 sequence_alteration RefSeqFE [{'db': 'dbSNP', 'id': '1570113'}, {'db': 'Gen... None [COORDINATES:natural variation mutant evidence... sequence alteration%3B rs1570113 (also known a...
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 236260355 236260355 <NA> id-GeneID:107548103-5 sequence_alteration RefSeqFE [{'db': 'dbSNP', 'id': '74149540'}, {'db': 'Ge... None [COORDINATES:natural variation mutant evidence... sequence alteration%3B rs74149540 (also known ...
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000003.11 1709521 1709521 <NA> id-GeneID:107522035-7 sequence_alteration RefSeqFE [{'db': 'dbSNP', 'id': '62262631'}, {'db': 'Ge... None [COORDINATES:natural variation mutant evidence... sequence alteration%3B rs62262631 A>G%2C hotsp...
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000004.11 41748007 41748007 <NA> id-GeneID:110011216-8 sequence_alteration RefSeqFE [{'db': 'GeneID', 'id': '110011216'}] None [COORDINATES:natural variation mutant evidence... sequence alteration%3B rs17884724 T>G%2C haplo...
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000004.11 74301817 74301817 <NA> id-GeneID:111832670-43 sequence_alteration RefSeqFE [{'db': 'dbSNP', 'id': '587776861'}, {'db': 'G... None [COORDINATES:natural variation mutant evidence... sequence_alteration%3B A allele at rs587776861...

Description

Section titled “Description”

RefSeq sequence change and assembly artifact intervals, one row per interval.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.20'
    • 'GCF_000001635.27'
    • 'GCF_009914755.1'

Schema

Section titled “Schema”
Column Type Description
sources STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[] Source provenance for the row.
assembly_accession TEXT Partition column. Versioned RefSeq assembly accession (GCF accession).
sequence_accession TEXT Versioned RefSeq nucleotide sequence accession on which the alteration is located; joins refseq.assembly_sequences.sequence_accession.
start INT 1-based inclusive start coordinate of the alteration interval.
end INT 1-based inclusive end coordinate of the alteration interval.
is_forward_strand BOOLEAN Whether the alteration interval is on the forward strand; null when the GFF strand is unspecified.
sequence_alteration_id TEXT Local GFF3 ID of the alteration; not a stable RefSeq identifier.
alteration_type TEXT Source GFF3 alteration 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.
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.
note TEXT Free text GFF Note annotation, if supplied.