Answer: The "female" DNA sequence is incomplete because it lack DNA from the Y chromosome.
A recent press release from the Leiden University (Netherlands) proclaims Leiden scientists sequence first female DNA.
This is a well-deserved winner of Jonathan Eisen's second Genomics by Press Release Award [Genomics By Press Release Award #2: Lieden University and the First "Female" Genome]. Read the award persentation speech on his blog The Tree of Life.
Congratulations to Leiden University1 for showing us how science should not be done and how science journalism is taking over from peer review publication.2.
1. "Leiden University is the oldest university in the Netherlands. It was founded in February 1575, as a gift from William of Orange to the citizens of Leiden who had withstood a long siege by the Spaniards."
2. We look forward to more press releases when the data is actually published in the peer reviewed literature.