chromEnd

ChromEnd is a genomic coordinate that marks the end position of a feature on a chromosome. It is commonly found as a field in BED-format files and in tracks produced by the UCSC Genome Browser. Along with chromStart, chromEnd defines the span of a genomic interval.

Coordinate conventions differ by format. In BED, both chromStart and chromEnd are 0-based, with chromEnd being exclusive. The interval covers the bases from chromStart up to chromEnd minus one, and the length is chromEnd - chromStart. For example, chromStart=1000 and chromEnd=1050 describes a 50-base region from 1000 to 1049 in 0-based coordinates; in 1-based coordinates this corresponds to 1001–1050.

In formats such as GFF and GTF, coordinates are 1-based and end-inclusive, so the end coordinate is counted in the feature length. When converting data between formats, the end coordinates must be adjusted to preserve the same biological region.

Usage: chromEnd marks the boundary of a feature for visualization, overlap calculations, and interval queries. It is a property of the genomic interval and is independent of strand orientation, which describes the direction of transcription rather than the end position in the genome.

Common issues include inconsistent coordinate systems across tools, off-by-one errors when interpreting chromEnd, and ensuring the correct genome assembly is used for comparisons.