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Jake had five fingers because he was an avatar, not an actual Na'vi. The avatars are made from a combination of human and Na'vi DNA, therefore, the common traits that a human possesses that an avatar doesn't (eyebrows and a fifth finger) were put into the avatar body, thus distinguishing the avatars from the Na'vi. The Na'vi are born with only four fingers and no eyebrows, that is the difference between avatars and Na'vi. When Jake's mind and soul were transferred into his avatar body forever, he kept his fifth finger and eyebrows because he was born as a human and the avatar was created with them, whereas if a human COULD (which they can't) have their mind and soul transferred into an actual Na'vi body, they would have four fingers and no eyebrows because the Na'vi were born with them.

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