I'm assuming that the reason that when you use eagle vision and you can see people in red and blue is because of their blood flowing through their veins. The DNA in their bodies has distincitve markers that say if their an Assassin or a Templar. That's why when you use Eagle Vision on Vidic and Lucy at the end of AC I, Lucy shows up as blue and Vidic as Red.
So when you use eagle vision in your room, that's why it's red. Subject 16 is a templar. I knew that Altair had a child with a templar woman and that's where Desmond's and Subject 16's line crosses but is it possible that Subject 16 is alive and he faked his death? Do you think Subject 16 is actually a templar? Trying to kill Desmond?