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Genomic copy number is the count of copies of a specified DNA sequence in a defined biological unit, such as a cell or a haploid-equivalent genome. The sequence and denominator matter: a two-copy autosomal locus in a diploid cell is one copy per haploid genome, while a deletion or duplication can alter that locus without changing the ploidy of the whole cell. Such segment-level differences underlie copy number variation.^[ref]

DNA replication also changes the number of DNA molecules during the cell cycle. A replicated chromosome contains sister copies without thereby becoming two independently counted chromosomes under the usual centromere-based convention. Report the cell-cycle stage when comparing absolute DNA copies per cell.

Sequencing depth can estimate relative genomic copy number by comparing coverage with a reference region, but library preparation, sequence-dependent mapping and population mixtures affect that comparison. In a hypothetical mixture where half the cells carry two copies and half carry four, the mean is three copies per cell; that average does not show that any individual cell carries three. Genomic copy number also differs from the number of expressed RNA or protein molecules. This distinction matters when connecting gene dosage to a molecular abundance model.

Sequencing depth describes the amount of sequence observation obtained, but its exact convention depends on the assay. For a genome, nominal mean depth can be approximated by total sequenced bases divided by target length; in RNA sequencing, depth often means the number of reads generated. Larger depth improves sampling of rare material but does not fix systematic bias or substitute for biological replication. ^[ref]

Whole-genome sequencing aims to sample sequence across an entire genome, rather than a selected panel or expressed subset. The label describes intended scope, not guaranteed complete observation of every base. Repeats, uneven representation and insufficient sequencing depth can leave regions unresolved. Analysis can involve mapping to a reference or genome assembly, and variants absent from the reference can require special attention. ^[ref]