Paternity

A mother has a child, with Man A, she gets pregnant 9 months later with her second child, whom she claims he be man B, Man A believes that the second child is his aswell, But the 2 children grow up in different house holds and never grew up together. They know that they are sisters but had a lot of controversy.

If the 2 sisters decide to get a DNA Test and it turns out the father is not the same ? What would the result be? And if the 2 sisters are exactly full blooded would that be a 99.9 percent chance of the 2 children having the same father ?