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bedrock.bio

refseq.alignments

import bedrock_bio as bb

rel = bb.load_table('refseq.alignments')
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 sequence_accession start end score is_forward_strand alignment_id alignment_type annotation_method ... mismatch_count target_coverage_fraction gapped_identity_fraction gap_open_identity_fraction ungapped_identity_fraction rank bit_score e_value is_curated_alignment not_for_annotation_code
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 20398 21446 1049.0 True cbaa27a6-261d-4cde-a2d2-47fa634f930b match RefSeq ... 0 1.0 1.0 1.0 1.0 1 1953.30 0.0 <NA> <NA>
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 52353 53496 1144.0 True f44de988-f66d-4059-a083-42aaa0da28cf match RefSeq ... 0 1.0 1.0 1.0 1.0 1 2130.10 0.0 <NA> <NA>
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 62916 63985 1070.0 True 97d4de9b-3480-4524-b512-8098b350b20a match RefSeq ... 0 1.0 1.0 1.0 1.0 1 1992.38 0.0 <NA> <NA>
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 126542 129325 2784.0 True 1dab45d8-19fa-4a25-9b29-44108685dad8 match RefSeq ... 0 1.0 1.0 1.0 1.0 1 5182.27 0.0 <NA> <NA>
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 130968 134936 3969.0 True ddd9180a-fe80-49c2-bd7d-183b78c783d1 match RefSeq ... 0 1.0 1.0 1.0 1.0 1 7387.64 0.0 <NA> <NA>

Description

Section titled “Description”

RefSeq sequence-to-assembly alignment blocks, one row per block.

Rows sharing an alignment_id are blocks of the same alignment. sequence_accession, start, and end locate the block on the assembly; the target_* fields locate its mapped interval on the aligned sequence.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.20'
    • 'GCF_000001635.27'
    • 'GCF_000001895.5'
    • 'GCF_000002035.5'
    • 'GCF_000002035.6'
    • 'GCF_000002285.3'
    • 'GCF_000002285.5'
    • 'GCF_000003025.5'
    • 'GCF_000003025.6'
    • 'GCF_000003195.3'
    • 'GCF_000003625.3'
    • 'GCF_000004195.4'
    • 'GCF_000004515.5'
    • 'GCF_000004515.6'
    • 'GCF_000151735.1'
    • 'GCF_000188115.5'
    • 'GCF_000215625.1'
    • 'GCF_000226075.1'
    • '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_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_accession TEXT Versioned RefSeq nucleotide sequence accession on which the alignment block is annotated; joins refseq.assembly_sequences.sequence_accession.
start INT 1-based inclusive start coordinate of the alignment block on sequence_accession.
end INT 1-based inclusive end coordinate of the alignment block on sequence_accession.
score DOUBLE GFF alignment score, if supplied; its definition varies by alignment type and source.
is_forward_strand BOOLEAN Whether the alignment block is on the forward strand of sequence_accession; null when unspecified.
alignment_id TEXT Local GFF3 ID of the alignment; shared by blocks of a multi-block alignment and not a stable identifier.
alignment_type TEXT Source GFF3 alignment type.
annotation_method TEXT NCBI GFF column-2 annotation method or source, if supplied.
target_accession TEXT Versioned accession of the aligned target sequence from the GFF Target attribute.
target_start INT 1-based inclusive start coordinate of the block on target_accession.
target_end INT 1-based inclusive end coordinate of the block on target_accession.
is_target_forward_strand BOOLEAN Whether the target interval is in forward orientation.
gap TEXT Exonerate CIGAR-like GFF Gap edit script describing indels in the alignment block, if supplied.
gap_count INT Number of gap openings in the whole alignment from GFF gap_count, if supplied.
identity_count INT Number of matching bases in the whole alignment from GFF num_ident, if supplied.
mismatch_count INT Number of mismatching bases in the whole alignment from GFF num_mismatch, if supplied.
target_coverage_fraction FLOAT Gapped target sequence coverage from GFF pct_coverage, normalized from percent to a fraction from 0 through 1, if supplied.
gapped_identity_fraction FLOAT Standard gapped alignment identity from GFF pct_identity_gap, normalized from percent to a fraction from 0 through 1, if supplied.
gap_open_identity_fraction FLOAT Alignment identity from GFF pct_identity_gapopen_only, counting every gap as one mismatch, normalized from percent to a fraction from 0 through 1, if supplied.
ungapped_identity_fraction FLOAT Alignment identity from GFF pct_identity_ungap, excluding gaps, normalized from percent to a fraction from 0 through 1, if supplied.
rank INT Source rank of this alignment among alternatives, if supplied.
bit_score DOUBLE BLAST bit score from GFF bit_score, if supplied.
e_value DOUBLE BLAST expectation value from GFF e_value, if supplied.
is_curated_alignment BOOLEAN Whether GFF curated_alignment=1 marks the alignment as curated; null when the source does not supply the attribute.
not_for_annotation_code Int8 Numeric GFF not_for_annotation status code, if supplied; values 1 and 2 are observed and its detailed semantics are not documented by NCBI.