According to the UN Population Fund, there were more than 8,000 cases of sexual violence in North and South Kivu last year. Their press statement is here, and Radio Okapi reported that there were 11,000 in all of the eastern Congo (N & S Kivu + Katanga, Maniema, Province Orientale). But it isn't clear if this is an estimate of total cases of sexual violence or actually recorded cases. I would imagine the total number to be much higher.
As a comparison, for the Kivus that would be a prevalence of around 0.9 cases/1000, lower than the rape rate in South Africa, which is around 1,2/1,000, and three times the rate in the United States. (See here for UN statistics.) Of course, any statistics with regards to sexual violence have to be taken with a bag of salt, for obvious reasons.