ensembl.chromosomes

Python
R

import bedrock_bio as bb

rel = bb.load_table('ensembl.chromosomes')
rel = rel.filter("genbank_assembly_accession = 'GCA_000001405.29'")

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()

	sources	release	genbank_assembly_accession	chromosome	aliases	is_circular	start_position	end_position	chromosome_source
0	[{'url': 'https://ftp.ensembl.org/pub/release-...	116	GCA_000001405.29	1	[CM000663.2, chr1, NC_000001.11]	<NA>	1	248956422	GRCh38
1	[{'url': 'https://ftp.ensembl.org/pub/release-...	116	GCA_000001405.29	10	[CM000672.2, chr10, NC_000010.11]	<NA>	1	133797422	GRCh38
2	[{'url': 'https://ftp.ensembl.org/pub/release-...	116	GCA_000001405.29	11	[CM000673.2, chr11, NC_000011.10]	<NA>	1	135086622	GRCh38
3	[{'url': 'https://ftp.ensembl.org/pub/release-...	116	GCA_000001405.29	12	[CM000674.2, chr12, NC_000012.12]	<NA>	1	133275309	GRCh38
4	[{'url': 'https://ftp.ensembl.org/pub/release-...	116	GCA_000001405.29	13	[CM000675.2, chr13, NC_000013.11]	<NA>	1	114364328	GRCh38

library(bedrockbio)
library(dplyr)

lf <- load_table("ensembl.chromosomes")
df <- filter(lf, genbank_assembly_accession == "GCA_000001405.29") |> collect()

head(df)

Sample output (5 rows, showing 7 of 9 columns)
   genbank_assembly_accession | release | chromosome | is_circular | start_position | end_position | chromosome_source
   -------------------------- | ------- | ---------- | ----------- | -------------- | ------------ | -----------------
0  GCA_000001405.29           | 116     | 1          | —           | 1              | 248956422    | GRCh38
1  GCA_000001405.29           | 116     | 10         | —           | 1              | 133797422    | GRCh38
2  GCA_000001405.29           | 116     | 11         | —           | 1              | 135086622    | GRCh38
3  GCA_000001405.29           | 116     | 12         | —           | 1              | 133275309    | GRCh38
4  GCA_000001405.29           | 116     | 13         | —           | 1              | 114364328    | GRCh38

Description

Reference chromosome intervals and their Ensembl GFF3 aliases.

One row per chromosome.

Always filter on genbank_assembly_accession. chromosome is the raw GFF3 sequence ID for these records; it is known to be a chromosome rather than a scaffold or contig.

Partitions

genbank_assembly_accession
- 'GCA_000001405.29'
- 'GCA_000001635.9'
- 'GCA_000001735.1'
- 'GCA_000002035.4'
- 'GCA_000002525.1'
- 'GCA_000002945.2'
- 'GCA_000002985.3'
- 'GCA_000003195.3'
- 'GCA_000003625.1'
- 'GCA_000004515.4'
- 'GCA_000005845.2'
- 'GCA_000006745.1'
- 'GCA_000006885.1'
- 'GCA_000007785.1'
- 'GCA_000008525.1'
- 'GCA_000009045.1'
- 'GCA_000009085.1'
- 'GCA_000009205.2'
- 'GCA_000011065.1'
- 'GCA_000016305.1'
- 'GCA_000025565.1'
- 'GCA_000027005.1'
- 'GCA_000027305.1'
- 'GCA_000146045.2'
- 'GCA_000149245.3'
- 'GCA_000196035.1'
- 'GCA_000226075.1'
- 'GCA_000409795.2'
- 'GCA_001433935.1'
- 'GCA_001704415.1'
- 'GCA_018294505.1'
- 'GCA_902167145.1'

Schema

Column	Type	Description
`sources`	`STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]`	Provenance for the GFF3 feature records.
`release`	`TEXT`	Ensembl release number the annotation was drawn from.
`genbank_assembly_accession`	`TEXT`	Partition column. GenBank assembly accession.
`chromosome`	`TEXT`	Ensembl chromosome name from the GFF3 sequence ID (e.g. `1`, `X`, or `MT`).
`aliases`	`TEXT[]`	Alternate chromosome names from the comma-separated GFF3 `Alias` attribute, including INSDC accessions when supplied.
`is_circular`	`BOOLEAN`	Whether the GFF3 `Is_circular` attribute marks the chromosome as circular. May be null when the attribute is absent.
`start_position`	`INT`	1-based start coordinate of the chromosome interval.
`end_position`	`INT`	1-based end coordinate of the chromosome interval.
`chromosome_source`	`TEXT`	Annotation source in GFF3 column 2 (often the assembly name).