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bedrock.bio

refseq.genomic_gaps

import bedrock_bio as bb

rel = bb.load_table('refseq.genomic_gaps')
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_accession start end gap_length gap_type linkage_evidence
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004353.4 1200663 1217662 17000 within_scaffold map
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004354.4 21907216 21907315 100 within_scaffold map
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004354.4 22260555 22260654 100 within_scaffold map
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004354.4 22281173 22281192 20 within_scaffold clone_contig
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004354.4 22282924 22314923 32000 within_scaffold clone_contig

Description

Section titled “Description”

Gap intervals in top-level RefSeq genomic sequences.

Each row describes one sequence interval occupied by a gap, including its NCBI gap type and linkage evidence.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001215.4'
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.20'
    • 'GCF_000001635.27'
    • '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_000002855.4'
    • 'GCF_000002945.1'
    • 'GCF_000002945.2'
    • 'GCF_000003025.5'
    • 'GCF_000003025.6'
    • 'GCF_000003195.3'
    • 'GCF_000003625.3'
    • 'GCF_000004195.4'
    • 'GCF_000004515.5'
    • 'GCF_000004515.6'
    • 'GCF_000006565.2'
    • 'GCF_000006665.1'
    • 'GCF_000027005.1'
    • 'GCF_000149245.1'
    • 'GCF_000151735.1'
    • 'GCF_000167675.1'
    • 'GCF_000182965.3'
    • 'GCF_000188115.5'
    • 'GCF_000215625.1'
    • 'GCF_000226075.1'
    • 'GCF_000237925.1'
    • 'GCF_000349665.1'
    • 'GCF_000364345.1'
    • 'GCF_000409795.2'
    • 'GCF_001433935.1'
    • '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_011100685.1'
    • 'GCF_016699485.2'
    • 'GCF_016772045.2'
    • 'GCF_017654675.1'
    • 'GCF_018294505.1'
    • 'GCF_020379485.1'
    • 'GCF_034190915.1'
    • 'GCF_036323735.1'
    • 'GCF_047675955.1'
    • 'GCF_049354715.1'
    • '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_accession TEXT Versioned RefSeq accession of the top-level sequence containing the gap; joins refseq.assembly_sequences.sequence_accession.
start INT 1-based inclusive start coordinate of the gap on sequence_accession.
end INT 1-based inclusive end coordinate of the gap on sequence_accession.
gap_length INT Length of the gap in base pairs, as reported by NCBI.
gap_type TEXT NCBI classification of the gap, such as within_scaffold, between_scaffolds, telomere, heterochromatin, short_arm, or unknown.
linkage_evidence TEXT NCBI evidence supporting the gap, such as paired-ends, within_clone, map, inferred_from_sequence, clone_contig, or unspecified; null when NCBI reports na.