Looking at (e.g.) my own user page, I'm listed as "top 0.89% overall". As I'm no. 5 of >5000 users at the moment, this should be "top 0.089% overall".
AFAIK only users with more than 200rep are taken into account. The rest don't count yet as full site members. If you go to http://stackexchange.com/leagues/29/ you will see in the right side bar that only about 10% of the users have 200rep or more, which explains the factor of 10.