Skip to content
bedrock.bio

refseq.assembly_sequences

import bedrock_bio as bb

rel = bb.load_table('refseq.assembly_sequences')
rel = rel.filter("assembly_accession = 'GCF_000001215.4'")

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources assembly_accession sequence_name sequence_role assigned_molecule assigned_molecule_location_type genbank_sequence_accession relationship sequence_accession unit_name sequence_length ucsc_name
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 211000022278031 unplaced-scaffold None None DS485919.1 = NW_001847208.1 Primary Assembly 1021 chrUn_DS485919v1
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 211000022278032 unplaced-scaffold None None DS483755.1 = NW_001845044.1 Primary Assembly 6936 chrUn_DS483755v1
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 211000022278033 unplaced-scaffold None None DS485425.1 = NW_001846714.1 Primary Assembly 1143 chrUn_DS485425v1
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 211000022278038 unplaced-scaffold None None DS484861.1 = NW_001846150.1 Primary Assembly 1395 chrUn_DS484861v1
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 211000022278047 unplaced-scaffold None None DS484484.1 = NW_001845773.1 Primary Assembly 2020 chrUn_DS484484v1

Description

Section titled “Description”

Sequence records in RefSeq genome assemblies, one row per assembly sequence.

Maps NCBI sequence names to versioned RefSeq and GenBank accessions.

Includes primary assembled molecules, alternate loci, unlocalized sequences, and unplaced sequences.

To map chromosomes, select rows where sequence_role is assembled-molecule.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001215.4'
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.20'
    • 'GCF_000001635.27'
    • 'GCF_000001735.3'
    • 'GCF_000001735.4'
    • 'GCF_000001895.5'
    • 'GCF_000002035.5'
    • 'GCF_000002035.6'
    • 'GCF_000002285.3'
    • 'GCF_000002285.5'
    • 'GCF_000002525.2'
    • 'GCF_000002655.1'
    • 'GCF_000002765.6'
    • 'GCF_000002855.4'
    • 'GCF_000002945.1'
    • 'GCF_000002945.2'
    • 'GCF_000002985.6'
    • 'GCF_000003025.5'
    • 'GCF_000003025.6'
    • 'GCF_000003195.3'
    • 'GCF_000003625.3'
    • 'GCF_000004195.4'
    • 'GCF_000004515.5'
    • 'GCF_000004515.6'
    • 'GCF_000005845.2'
    • 'GCF_000006565.2'
    • 'GCF_000006665.1'
    • 'GCF_000006745.1'
    • 'GCF_000006765.1'
    • 'GCF_000006845.1'
    • 'GCF_000006885.1'
    • 'GCF_000006925.2'
    • 'GCF_000006945.2'
    • 'GCF_000007545.1'
    • 'GCF_000007565.2'
    • 'GCF_000007785.1'
    • 'GCF_000008525.1'
    • 'GCF_000008765.1'
    • 'GCF_000008805.1'
    • 'GCF_000009045.1'
    • 'GCF_000009085.1'
    • 'GCF_000009205.2'
    • 'GCF_000011065.1'
    • 'GCF_000011325.1'
    • 'GCF_000013425.1'
    • 'GCF_000013465.1'
    • 'GCF_000015005.1'
    • 'GCF_000016305.1'
    • 'GCF_000025565.1'
    • 'GCF_000025985.1'
    • 'GCF_000027005.1'
    • 'GCF_000027305.1'
    • 'GCF_000146045.2'
    • 'GCF_000149245.1'
    • 'GCF_000151735.1'
    • 'GCF_000167675.1'
    • 'GCF_000174395.2'
    • 'GCF_000182965.3'
    • 'GCF_000188115.5'
    • 'GCF_000195715.1'
    • 'GCF_000195955.2'
    • 'GCF_000195995.1'
    • 'GCF_000196035.1'
    • 'GCF_000196095.1'
    • 'GCF_000203835.1'
    • 'GCF_000215625.1'
    • 'GCF_000226075.1'
    • 'GCF_000237925.1'
    • 'GCF_000285655.3'
    • 'GCF_000306945.1'
    • 'GCF_000349665.1'
    • 'GCF_000364345.1'
    • 'GCF_000409795.2'
    • 'GCF_000767705.1'
    • 'GCF_000805365.1'
    • 'GCF_001077675.1'
    • 'GCF_001433935.1'
    • 'GCF_001457595.1'
    • 'GCF_001593425.2'
    • 'GCF_001704415.1'
    • 'GCF_001704415.2'
    • 'GCF_001858045.2'
    • 'GCF_002263795.3'
    • 'GCF_002759435.1'
    • 'GCF_002863925.1'
    • 'GCF_003339765.1'
    • 'GCF_003668045.3'
    • 'GCF_007990345.1'
    • 'GCF_008728515.1'
    • 'GCF_009914755.1'
    • 'GCF_011100685.1'
    • 'GCF_011764305.1'
    • 'GCF_016699485.2'
    • 'GCF_016772045.2'
    • 'GCF_017654675.1'
    • 'GCF_018294505.1'
    • 'GCF_020379485.1'
    • 'GCF_034190915.1'
    • 'GCF_036323735.1'
    • 'GCF_037993035.2'
    • 'GCF_047675955.1'
    • 'GCF_049350105.2'
    • 'GCF_049354715.1'
    • 'GCF_052040795.1'
    • 'GCF_054392235.1'
    • 'GCF_902167145.1'
    • 'GCF_905237065.1'
    • 'GCF_964237555.1'

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_name TEXT NCBI sequence name within the assembly, such as 1, X, MT, or a scaffold name.
sequence_role TEXT NCBI role assigned to the sequence, such as assembled-molecule, unlocalized-scaffold, or unplaced-scaffold.
assigned_molecule TEXT Chromosome or other assigned molecule, if NCBI provides one.
assigned_molecule_location_type TEXT NCBI location/type of the assigned molecule, such as Chromosome.
genbank_sequence_accession TEXT Versioned GenBank sequence accession, if supplied.
relationship TEXT NCBI relationship between the RefSeq and GenBank sequence records, if supplied.
sequence_accession TEXT Versioned RefSeq sequence accession; use this identifier for resources that use RefSeq accessions, such as dbSNP VCF contig names.
unit_name TEXT NCBI assembly unit containing the sequence, such as Primary Assembly or PATCHES.
sequence_length BIGINT Sequence length in base pairs.
ucsc_name TEXT UCSC-style sequence name, if NCBI provides one.