What fraction of sites are expected to be polymorphic?
The fraction of polymorphic sites that exist in a population is dependent on the biology of the organism. For instance, you would expect to find different rates of polymorphism in related plants that have different breeding systems, e.g. in Silene [1]. Past bottlenecks are also expected to decrease polymorphisms [2]. So, the answer to your question would depend on the exact species and population that you are looking at.