Cytoband

The Cytoband file format is used to specify the cytobands for an imported genome. IGV uses this file to draw the chromosome ideograms for the genome.

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 CytoBank table in the database underlying the UCSC Genome Browser (http://genome.ucsc.edu/):

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