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There is no such thing as a LEGIT Shiny Manaphy, just so you know....
From Project Pokemon:There is no such thing as a LEGIT Shiny Manaphy, just so you know....
Preventing Manaphy from hatching shiny is a bit more tricky since you are allowed to trade your egg. It turns out Game Freak overlooked something and obtaining a legit shiny manaphy is possible, albeit very difficult. In this case the shiny check is not done at the time when the PID is generated. This would not have worked since upon hatching the pokemon receives the ID/Secret ID of the trainer who hatches the egg. Instead the PID is generated using the PRNG and the normal algorithm and the shiny check is called at the time of hatching. When an egg is about to hatch the game checks whether the pokémon inside the egg is manaphy, if so, the shiny check is called until the game is sure the PID/ID/Secret ID don't combine to give you a shiny manaphy. This prevents most manaphy from being shiny. However, the way the shiny check works is that it uses the PID, ID and Secret ID currently on the pokémon and the ID and Secret ID of the trainer hatching the egg does not get written to the pokémon until after the shiny check has gone through. This means that if you trade your manaphy egg to a friend there is a chance that it will hatch shiny, and if your friend trades you a manaphy egg it might hatch shiny. But if you don't trade the egg it will NOT hatch shiny.