^aThe total number of polymorphisms found in the rDNA is dependent on the coverage level. Therefore, observed polymorphisms were corrected to “real” polymorphism number using genome coverage level. All single-read polymorphisms were included as single-copy polymorphisms, and only high-confidence polymorphisms were used (e.g., we calculated a total of 40 polymorphic sites in C. neoformans among the 55 copies).

^bThe fold increase of poly-u repeat π relative to rDNA repeat π.

^cThe value of π when only polymorphisms present on more than one sequence read are counted.