hg19chromsizes

hg19chromsizes refers to the chromSizes file for the human genome assembly known as hg19 (also called GRCh37). It is a plain text resource that lists chromosome identifiers and their lengths in base pairs, typically in two columns: chromosome name and size. For hg19, the standard set includes the 22 autosomes plus X, Y, and often the mitochondrial chromosome (chrM). Some distributions may also include unplaced contigs or alternative sequences; others may provide a streamlined set containing only the primary chromosomes.

The chromSizes file defines the reference coordinate system used in many genomic workflows. It provides the upper bounds for each chromosome, enabling operations such as interval calculations, genome-wide plotting, and normalization of sequencing coverage. It is commonly used by tools for read counting, binning, and visualization in both command-line pipelines and software environments (for example BEDTools, deepTools, and genome browsers), and it serves as a reference for constructing genome-wide bins or performing per-chromosome analyses.

Source and generation: hg19chromsizes is typically distributed by the UCSC Genome Browser in the hg19/bigZips directory as hg19.chrom.sizes. It can also be generated from the hg19 FASTA index (faidx) or other sequence references using standard bioinformatics tools. The term hg19 corresponds to the historical hg19 version of the human genome assembly, with GRCh37 as its official nomenclature; many pipelines use these terms interchangeably.

Overall, hg19chromsizes provides a concise, machine-readable map of chromosome lengths for the hg19 genome assembly, supporting a wide range of downstream genomic analyses.