dbsnp.frequencies

Python

In [1]:

import bedrock_bio as bb

rel = bb.load_table('dbsnp.frequencies')
rel = rel.filter("assembly_accession = 'GCF_000001405.25' AND chromosome = '1'")

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

Out[1]:

	sources	build	assembly_accession	assembly_name	chromosome	position	ref_allele	alt_allele	rsid	study	alt_allele_frequency
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	10001	T	A	rs1570391677	KOREAN	0.010900
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	10001	T	A	rs1570391677	SGDP_PRJ	1.000000
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	10001	T	C	rs1570391677	dbGaP_PopFreq	0.000000
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	10002	A	C	rs1570391692	KOREAN	0.005597
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	10003	A	C	rs1570391694	KOREAN	0.009763

R

In [1]:

library(bedrockbio)
library(dplyr)

lf <- load_table("dbsnp.frequencies")
df <- filter(lf, assembly_accession == "GCF_000001405.25", chromosome == "1") |> collect()

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 11 columns)
   assembly_accession | chromosome | build | assembly_name | position | ref_allele | alt_allele | rsid
   ------------------ | ---------- | ----- | ------------- | -------- | ---------- | ---------- | ------------
0  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 10001    | T          | A          | rs1570391677
1  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 10001    | T          | A          | rs1570391677
2  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 10001    | T          | C          | rs1570391677
3  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 10002    | A          | C          | rs1570391692
4  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 10003    | A          | C          | rs1570391694

Description

Alternate allele frequencies reported by population genetics studies, from the dbSNP FREQ annotation.

Frequencies are reported by the source study for each rsid.

A value of zero means the study genotyped the allele but did not observe it; no row means the study did not report it for that rsID.

Partitions

• assembly_accession
  • 'GCF_000001405.25'
  • 'GCF_000001405.40'
• chromosome
  • '1'
  • '10'
  • '11'
  • '12'
  • '13'
  • '14'
  • '15'
  • '16'
  • '17'
  • '18'
  • '19'
  • '2'
  • '20'
  • '21'
  • '22'
  • '3'
  • '4'
  • '5'
  • '6'
  • '7'
  • '8'
  • '9'
  • 'MT'
  • 'X'
  • 'Y'

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Source provenance for the row.
build	TEXT	dbSNP build version (e.g. b157).
assembly_accession	TEXT	Partition column. Versioned RefSeq assembly accession (GCF) for the variant coordinates.
assembly_name	TEXT	Exact NCBI assembly name, including its patch release (for example, GRCh38.p14).
chromosome	TEXT	Partition column. Chromosome on which the variant is located (1-22, X, Y, MT).
position	INT	Variant position within the chromosome (1-based).
ref_allele	TEXT	Reference allele.
alt_allele	TEXT	Alternate allele.
rsid	TEXT	NCBI RefSNP identifier.
study	TEXT	Study or project that reported the frequency, as named by dbSNP (e.g. TOPMED, GnomAD_genomes, 1000Genomes, dbGaP_PopFreq, ALFA).
alt_allele_frequency	DOUBLE	Frequency of alt_allele in the study, between 0 and 1.