If you are really concerned about the genetics of the babies, you shouldn't have bought a petstore mouse in the first place. You don't know afterall, the genetics of the mother either. The babies could be just as healthy or unhealthy as the mother.
If you already knew the mouse was pregnant in the first place probably would have been best not to buy her at all if you didn't want to raise the young in the first place. If you were hoping to use the young for something other than pets or breeding then the genetics won't matter anyway.
Just separate the sexes when the babies are about 4 weeks old and let them live if you want them just as pets. If you plan to do more breeding as a fancy mouse breeder (as opposed to say, a feeder mouse breeder) neither the babies or the mother would be suitable. For fancy mice breeding, better to find a local mouse breeder and buy from them. THis way you will know who is the mother and father, their parents etc for many generations, thus being very sure on the quality of genetics.