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The term genome can have different meanings. In this context, consider genome as the entire DNA (genetic material) contained within an individual cell of an organism. For example, the DNA of a human genome is organized into 22 (somatic) chromosomes — numbered from 1 to 22— plus the X and Y chromosomes. This totals 24 distinctly-sized chromosomes. The nuclei of most human cells contain the diploid genome which is 46 chromosomes (23 pairs): each somatic chromosome pairs with itself, while the X chromosome can either pair with itself (in females) or the Y chromosome (in males). In addition to the nuclear genome, a mitochondrion in the cell's cytoplasm carries its own genome.

When researchers set out to sequence a genome, they understand that they will generate a model of that genome rather than capture its exact being. This is particularly true for genomes of eukaryotic organisms (Taxonomy ID: 2759) that are generally more complex and more diverse between individuals of the same species than those belonging to prokaryotes (Archaea; Taxonomy ID: 2157 and Bacteria; Taxonomy ID: 2). Furthermore, while most eukaryotic organisms have diploid genomes (some plants can have even more than two copies of each of the chromosomes per nucleus), models often have a single-copy (haploid) representation. At NCBI, genome models are called genome assemblies or simply assemblies. An assembly can be defined as a collection of sequence records that represent a genome. More than one assembly may be available at NCBI for an individual organism (individual species).

See also the article on how different levels of assemblies are generated.