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Cytoband
The Cytoband file format is used to define the chromosome ideograms for a reference genome, and/or as of version 2.11.0 to create a cytoband track.
A cytoband file is a five-column tab-delimited text file. Each row of the file describes the position of a cytogenetic band. The columns in the file match the columns of the cytoBand table in the database underlying the UCSC Genome Browser. These files are downloadable from the UCSC website as "cytoBandIdeo.txt.gz" for many genome assemblies, for example https://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/cytoBandIdeo.txt.gz
| Column | Example | Data Type | Description |
|---|---|---|---|
| chrom | chr1 | string | Chromosome |
| chromStart | 0 | integer |
Start position in chromosome sequence |
| chromEnd | 2300000 | integer | End position in chromosome sequence |
| name | p36.33 | string | Name of cytogenetic band |
| gieStain | gneg | string | Giemsa stain results. Recognized stain values: gneg, gpos50, gpos75, gpos25, gpos100, acen, gvar, stalk |