"Millions of e-books that would have sold at retail for $[US]9.99 or for other low prices [by other retailers] instead sold for the prices indicated by the price schedules included in the Apple Agency Agreements - generally, $[US]12.99 or $[US]14.99."
The DoJ filing also says "Apple's entry into the e-book business provided a perfect opportunity for collective action [by the publishers] to implement the agency model and use it to raise retail e-book prices."
"Apple soon concluded, though, that competition from other retailers - especially Amazon - would prevent Apple from earning its desired 30 percent margins on e-book sales" and was therefore open to the publishers' offer of agency agreements, even though "Apple realized that, as a result of the scheme, 'the customer' would 'pay a little more.'"
Apple is also said to have insisted on the "most favoured nation" clause that ensured the publishers would lower the price of any ebook in the iBookstore if necessary to match that of any other retailer, while leaving Apple with its 30% cut.
The publishers actions are also alleged to have been at least in part a response to Amazon striking deals with authors for ebook editions of their work, cutting out traditional publishers.
Page 3: What the DoJ wants.