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Naruto's chakra colour is yellow. When he goes kyuubi mode it turns red.
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Your right and your wrong. When Naruto goes to chakra cloak it goes red but Minato set a seal that the Kyubis chakra leaks out and mixes with Naruto's which it has been. And Kakashi confirmed the root of Naruto's chakra is the kyubi and that's before drawing on It for the chakra cloak at that time it's yellow. The natural mixing of human and beast chakra takes a yellow tint this is also reflected in Naruto's KCM after he steals Kurama's chakra. It goes red when Naruto draws more than the natural mixing process so it takes on the colour of the Kyubis chakra.
I hope the post makes sense I'm on the phone and can't chop and change.