chromStart

ChromStart is a field used in genomic feature data to denote the starting position of a feature on a chromosome. It is defined using 0-based indexing, meaning that the first base on a chromosome is position 0. The end position is stored separately in a parallel field called chromEnd, and together they define the feature’s span.

In BED format, chromStart and chromEnd specify a half-open interval: the feature includes chromStart but excludes chromEnd. As a result, the length of the feature is chromEnd minus chromStart. For example, a feature spanning bases 1 through 100 inclusive (1-based coordinates) is represented as chromStart = 0 and chromEnd = 100, giving a length of 100 bases. If a feature covers bases 1000 through 2000 inclusive, it would be chromStart = 999 and chromEnd = 2000, with a length of 1001 bases.

ChromStart commonly appears as a column in BED files and related track data used by genome browsers and annotation pipelines, notably in the UCSC Genome Browser. It is essential for defining genomic intervals in many bioinformatics workflows, including feature annotation, peak calling outputs, and interval comparisons.

Coordinate conventions vary across formats. Formats like GFF/GTF typically use 1-based coordinates, so converting between 1-based and 0-based systems requires adjustment. Practitioners should verify the coordinate system used by their data source and tools to avoid off-by-one errors when interpreting chromStart and related fields.