Well, that's the point - you don't want them all deleted. You need the standard groups. If you run these queries, it'll put back the standard groups:
INSERT INTO `w3t_Groups` VALUES ('Administrators', 1, 0);
INSERT INTO `w3t_Groups` VALUES ('Moderators', 2, 0);
INSERT INTO `w3t_Groups` VALUES ('Users', 3, 0);
INSERT INTO `w3t_Groups` VALUES ('Guests', 4, 0);