He's not her father, his name was Johnny topside ( nickname given to him by rapture populace) he's a deep sea diver who found rapture all on his own and ryan believed he was a spy so he made Sinclair get rid of him basically turning him into a "volunteer" for the big daddy protector alpha series.
In the game she calls him father, he is the only father she remembers, even if he is a big daddy, she sees him as her father. It also helps that alpha series big daddies are bound to a single little sister, which may cause the little sisters to see the individual big daddy assigned to them as their parent, not like the new little sisters who dont exactly imprint on the bouncers or rosies. I dont remember sophia lamb getting impregnated with delta's sperm, could be wrong
I believe there was an audio diary that was cut from the game that confirmed Delta as the biological father. Though seeing as it was cut, that probably either means the idea was scrapped all together or they chose to leave it up to interpretation
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