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bedrock.bio

assembly_statistics

Identifier

Section titled “Identifier”
refseq.assembly_statistics

Description

Section titled “Description”

Assembly statistics from assembly-specific *_assembly_stats.txt reports.

Each row is scoped by assembly unit, molecule, molecule type or location, and sequence type.

Statistics are represented as columns.

Assembly unit accessions are obtained from the report’s Assembly-Units header using unit_name.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001215.4'
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.20'
    • 'GCF_000001635.27'
    • 'GCF_000001895.5'
    • 'GCF_000002035.6'
    • 'GCF_000002285.3'
    • 'GCF_000002985.6'
    • 'GCF_000003025.6'
    • 'GCF_000003625.3'
    • 'GCF_000005845.2'
    • 'GCF_000146045.2'
    • 'GCF_003339765.1'
    • 'GCF_012559485.2'
    • 'GCF_015227675.2'
    • 'GCF_036323735.1'
    • 'GCF_037993035.2'
    • 'GCF_049350105.2'
    • 'GCF_052040795.1'
    • 'GCF_054392235.1'
    • 'GCF_964237555.1'

Schema

Section titled “Schema”
Column Type Description
sources STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[] Original external inputs used to produce the row. Each item contains its source URL, filename, HTTP Last-Modified timestamp when available, and computed SHA-256 checksum.
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.