Gene copy number is a critical consideration in interpretation of mutant phenotypes and gene fitness. Tandem gene duplications within chromosomes of prokaryotic cells occur frequently but are generally unstable. Unless this increased copy number of genesprovides a fitness benefit that allows the cell to outgrow the rest of the population, it is not maintained. Thus, these gene amplifications are considered rare at the population level. However, analysis of discrepancies in sequencing depth has revealed that large tandem duplications occur frequently in microbial genomes, but are underrepresented in published genomes as they are missed during assembly.