I've never heard of the 1% figure, but it wouldn't surprise me. According to my university criminology text, it's estimated that only about one in twenty break and entry occurances result in someone being prosecuted (the text used that crime as an example of how the number of crimes that make it through each stage of the justice system decreases). That's five percent. If those are the stats for break and entry, it wouldn't surprise me at all if rape cases had even lower rates, since those are so often unreported.
It likely does vary by area, and by definition of rape.