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I've already synced my phone to iPhoto and emptied the camera roll.

There is no application data category listed that is more than 100 MB or so, and yet it says that the backup is 4.9 GB. There appears to be no user-servicible setting to reduce this.

This is with iOS 6.1 installed, but it was also noticeable with 6.0.

I tried also clearing out all Messages conversations. That did not help.

What the hell is my phone saving that's so huge?

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Are you trying to do an iCloud or an local/iTunes backup? – patrix Feb 7 '13 at 18:12
Are you by any chance looking under Settings > iCloud > Storage & Backup > Manage Store? Or, Settings > iCloud > Storage & Backup > Manage Store > "[your iPhone name] This iPhone"? Under the heading "Backup Options" of the later, you will see things that are occupying storage space. – bassplayer7 Feb 7 '13 at 19:03

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