When they are showing the names, around 0:26 in this video
http://www.youtube.com/watch?v=GUKwH81csts
I suppose if they are going for consistency (and it appears they do, if I am correct that would be the only overdub in the entire song), that would actually be the keyboard playing.
The bass is playing a very low "2 0 0" type pattern, while the guitar is playing two consecutive chords followed by two mute picks (creating a chk-chk sound).
The problem with the consistency is that at the very end there is a keyboard "sweep" which would make it impossible for the effect we are hearing to be played by the keyboard (as it is obviously doing something else).
In summary, it's either the keyboard or guitar, but whichever it is, there is inconsistency as it creates the need for one of the instruments to play two things at once. This does surprise me, as the ED video does trick you into thinking that it is totally inaccurate, as it appears Mio isn't playing anything and has her hand off of the neck while the bass is still actually playing. However, upon a few more second of observation, you can see they are cleverly hiding her picking hand, and since the bass is only playing open notes, her hand doesn't need to be anywhere near the neck. The biggest problem I have is when Mio seems to have a deathgrip on the neck of her guitar. I suppose it is possible to have your hand located correctly that low on the neck so that you could play those high notes in the correct order and all that without moving it, but I find it highly unlikely. I'll find out tomorrow when I tab out the song for myself.
Of course, none of this matters anyway XD
As a final thought, let me just say that they seem to be very good at hiding the guitar in the final mix of the song, only having it apparent when they want it to be, yet letting be played through out the entirety of both the OP and the ED. It's very easy to lose track of if you don't have a keen ear for instruments like that.