cytogenetic_bands: GRCh38 human cytogenetic bands.
In gwasrapidd: 'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

cytogenetic_bands

R Documentation

GRCh38 human cytogenetic bands.

Description

A dataset containing the GRCh38 human cytogenetic bands and their genomic coordinates.

Usage

cytogenetic_bands

Format

A data frame with 862 rows and 8 variables:

cytogenetic_band: Cytogenetic band name. See Cytogenetic Nomenclature below.
chromosome: Chromosome name: 1 through 22 (the autosomes), X or Y.
start: Genomic start position of the cytogenetic band. Starts at 1.
end: Genomic end position of the cytogenetic band. End position is included in the band interval.
length: Length of the genomic interval of cytogenetic band.
assembly: Assembly version, should be 'GRCh38'.
stain: Giemsa stain results: Giemsa negative, 'gneg'; Giemsa positive, of increasing intensities, 'gpos25', 'gpos50', 'gpos75', and 'gpos100'; centromeric region, 'acen'; heterochromatin, either pericentric or telomeric, 'gvar'; and short arm of acrocentric chromosomes 13, 14, 15, 21, and 22 are coded as 'stalk'.
last_download_date: Time stamp of last time this dataset was downloaded from Ensembl.

Details

Genomic coordinates are for fully closed intervals.

Cytogenetic Nomenclature

Cytogenetic bands are numbered from the centromere outwards in both directions towards the telomeres on the shorter p arm and the longer q arm.

The first number or letter represents the chromosome. Chromosomes 1 through 22 (the autosomes) are designated by their chromosome number. The sex chromosomes are designated by X or Y. The next letter represents the arm of the chromosome: p or q.

The numbers cannot be read in the normal decimal numeric system e.g. 36, but rather 3-6 (region 3 band 6). Counting starts at the centromere as region 1 (or 1-0), to 11 (1-1) to 21 (2-1) to 22 (2-2) etc. Subbands are added in a similar way, e.g. 21.1 to 21.2, if the bands are small or only appear at a higher resolution.