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bedrock.bio

refseq.assembly_regions

import bedrock_bio as bb

rel = bb.load_table('refseq.assembly_regions')
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 unit_accession genbank_unit_accession unit_name region_name chromosome chromosome_start chromosome_end scaffold_role genbank_sequence_accession sequence_accession
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 GCF_000005045.12 GCA_000005045.13 PATCHES REGION77 1 3823584 3845268 fix-patch JH806574.2 NW_004070864.2
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 GCF_000005045.12 GCA_000005045.13 PATCHES REGION60 1 31872759 32017063 fix-patch GL949741.1 NW_003571030.1
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 GCF_000005045.12 GCA_000005045.13 PATCHES 1P11 1 120471050 121346350 fix-patch JH636053.3 NW_003871056.3
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 GCF_000005045.12 GCA_000005045.13 PATCHES 1Q21 1 143871003 150440213 fix-patch JH636052.4 NW_003871055.3
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 GCF_000005045.12 GCA_000005045.13 PATCHES REGION2 1 153673007 153838214 novel-patch GL383518.1 NW_003315905.1

Description

Section titled “Description”

Genomic regions with alternate scaffold and patch placements, one row per named region.

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

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.20'
    • 'GCF_000001635.27'
    • 'GCF_000002035.6'
    • 'GCF_000003025.6'
    • 'GCF_002263795.3'
    • 'GCF_009914755.1'
    • 'GCF_016772045.2'

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).
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.