Whilst given a percentage of children born as a result of rape is impossible (many mothers would not have come forward as victims of rape for one reason or another), the commonly cited number of women raped by Soviet troops is around 1 million in the year or so after the occupation of Germany(Catherine Merridale - Ivan's War). However some of those who were victims of rape were then murdered as the easiest way to silence the victims.

The East German population at the end of the War was around 14-16 million (the vague number is due to the influx and egress of people from the east and to the west respectively constantly changing the population). With the female population making somewhat more than half of the population (due to male war deaths), you can conservatively say that around 1/7th or so of the female population of the Soviet occupation zone would have become victims of rape, of these some would have brought resulting pregnancies to term, so the probable number is maybe 100,000.

This really is an area where many people preferred to be silent over what happened, so there has to be a large amount of inference and all estimates are tentative at best.