This is the strongest lineup they could put out (the played more of a 'B' team vs Scotland), but they are missing quite a few players due to injury. They have a full strength front row, but are missing their two first choice locks (Vickermann and Horwill). The loose-forward trio is more or less at full strength. Where they have been particularly badly hit is at 10 - Quade Cooper has only just come back from injury and is sitting out this series, James O'Connor (who would also be an option at 12 or wing) is out with a lacerated kidney (sounds painful!), Kurtley Beale (normally their first choice 15) had been lined up to play 10, but is out with a shoulder injury, while Christian Lealiifano, who was in outstanding form at 10 for the top of the table Brumbies, is now out for the season with an ankle injury. It means Berrick Barnes is stuck playing 10 - while he is an experienced test player, he has been in very poor form this season. Because O'Connor and Beale are out, the rest of the backline has been rearranged somewhat. The midfield is more or less at full strength (though Ben Tapuai would have been close had he not been injured), and they do have some injuries in the outside backs, with Lachie Turner and Drew Mitchell out (though Mitchell has just returned for the Waratahs). Joe Tomane, who was initially picked to start on the right wing is now out injured too.
Overall I'd say they have 5-6 players missing from what would be their top XV, though they are down to about their 5th choice 10....