No one will give you the exact number. Some historians, for example, tells about 200,000 or even 700,000 killed in Novgorod, but at that time the entire population of the city was about 40,000. Hypocrites calls it reign bloody, forgetting about St. Bartholomew's Day massacre.
Historian Ruslan G. Skrynnikov (1931-2009) in his books «Начало опричнины» (1966), «Опричный террор» (1969), «Иван Грозный» (1975) gives the number of 3,000-4,000 repressed.
Very, very controversial leader, but no less controversial research of his reign.