= Gene copy number
<Gene copy number> is the count of copies of a specified <gene> sequence relative to a stated reference, such as one <genome> or one <biological cell>. The reference matters: the count per cell can change with the number of genome equivalents even when the count per genome is unchanged. A DNA copy count also differs from <gene expression> or the amount of its <protein> product.
A primary example is the <16S ribosomal RNA gene>. A2004 study compared gene copies and their sequence differences within bacterial and archaeal <genomes>. It showed why a marker's copy count and sequence diversity must be considered separately when interpreting community data.<Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons by Silvia G. Acinas and others>[Abstract and Introduction, copy-number distribution and intragenomic divergence]{ref}
For an invented ideal assay,200 cells of population A carry two target copies each, while100 cells of population B carry four each. Both supply400 templates, giving equal template shares despite cell shares of $2/3$ and $1/3$. More generally, a response can scale as $N_i k_i e_i$, where $N_i$ is cell count, $k_i$ copies per cell and $e_i$ combined recovery/amplification efficiency. Inferring cell numbers then requires information about the other factors. <Copy number variation> describes a biological source of changing counts; an assay response alone does not establish which source caused a difference.
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