The phrase "different alleles" refers to variations or different versions of a specific gene. Alleles can cause differences in traits or characteristics, like eye or hair color, in living organisms. Full definition
In humans, eye color is caused by different alleles of the «eye - color gene.» (optigen.com)
The predominant modern su1 allele was found in all of the older Mexican cobs, but the younger New Mexican cobs had several different alleles, suggesting that this gene was still undergoing selection when maize reached North America. (sciencemag.org)
It requires as input a list of chromosomes and coordinates, and returns the count for different alleles among the genomes it references. (completegenomics.com)