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bedrock.bio

refseq.assembly_statistics

import bedrock_bio as bb

rel = bb.load_table('refseq.assembly_statistics')
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 unit_accession genbank_unit_accession unit_name molecule_name molecule_type sequence_type component_count contig_count ... scaffold_n50 scaffold_l50 scaffold_n75 scaffold_n90 spanned_gap_count top_level_count total_gap_length total_length ungapped_length unspanned_gap_count
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 GCF_000001625.3 GCA_000001625.3 Primary Assembly 2L Chromosome all <NA> <NA> ... 23513712 <NA> <NA> <NA> 2 <NA> <NA> 23513712 23513512 0
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 GCF_000001625.3 GCA_000001625.3 Primary Assembly 2L Chromosome assembled-molecule <NA> <NA> ... 23513712 <NA> <NA> <NA> 2 <NA> <NA> 23513712 23513512 0
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 GCF_000001625.3 GCA_000001625.3 Primary Assembly 2L Chromosome unlocalized-scaffold <NA> <NA> ... 0 <NA> <NA> <NA> 0 <NA> <NA> 0 0 0
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 GCF_000001625.3 GCA_000001625.3 Primary Assembly 2R Chromosome all <NA> <NA> ... 25286936 <NA> <NA> <NA> 8 <NA> <NA> 25286936 25280236 0
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 GCF_000001625.3 GCA_000001625.3 Primary Assembly 2R Chromosome assembled-molecule <NA> <NA> ... 25286936 <NA> <NA> <NA> 8 <NA> <NA> 25286936 25280236 0

Description

Section titled “Description”

Assembly statistics, one row per assembly unit, molecule, molecule type or location, and sequence type.

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).
unit_accession TEXT Versioned RefSeq assembly unit accession from the report header, if unit_name identifies a specific unit.
genbank_unit_accession TEXT Versioned GenBank assembly unit accession from the report header, if unit_name identifies a specific unit.
unit_name TEXT Assembly unit name from the statistics report, such as Primary Assembly or PATCHES.
molecule_name TEXT Molecule scope from the report, such as a chromosome name, all, or na when no molecule is assigned.
molecule_type TEXT Molecule type or location scope from the report’s molecule-type/loc column, such as Chromosome, Mitochondrion, all, or na.
sequence_type TEXT Sequence scope from the report, such as all sequences, assembled molecules, unlocalized scaffolds, or unplaced scaffolds.
component_count BIGINT Number of sequence components.
contig_count BIGINT Number of contigs.
contig_n50 BIGINT Contig length in base pairs at which 50% of bases are in contigs at least that long.
contig_l50 BIGINT Number of contigs at least the contig N50 length.
gc_fraction DOUBLE GC bases divided by ATGC bases, normalized from NCBI’s gc-perc percentage to a fraction from 0 through 1.
molecule_count BIGINT Number of chromosomes and plasmids.
region_count BIGINT Number of defined genomic regions.
scaffold_count BIGINT Number of scaffolds.
scaffold_n50 BIGINT Scaffold length in base pairs at which 50% of bases are in scaffolds at least that long.
scaffold_l50 BIGINT Number of scaffolds at least the scaffold N50 length.
scaffold_n75 BIGINT Scaffold length in base pairs at which 75% of bases are in scaffolds at least that long.
scaffold_n90 BIGINT Scaffold length in base pairs at which 90% of bases are in scaffolds at least that long.
spanned_gap_count BIGINT Number of gaps within scaffolds.
top_level_count BIGINT Number of chromosomes or plasmids plus unplaced, unlocalized, alternate-locus, and patch scaffolds.
total_gap_length BIGINT Total gap length in base pairs.
total_length BIGINT Total sequence length in base pairs, including gaps.
ungapped_length BIGINT Total sequence length in base pairs, excluding gaps.
unspanned_gap_count BIGINT Number of gaps between scaffolds.