Meta-PokéBase Q&A
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Example: Ghostly Forest
Gastly: Common
Misdreavus: Uncommon
Phantump: Rare

Fishing:
Frillish (M): Common
Frillish (F): Common
Jellicent (M): Rare
Jellicent (F): Rare

Interact:
Giratina: Only one

Ya know, like that.

If you still dont understand, see [**this.**][1]
[1]: http://pokemondb.net/location/johto-ilex-forest

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I'm pretty sure the encounter rates are just estimates based on gameplay experience.

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Best answer

For all previous games it's based on data directly extracted from the game's code. All Pokemon have a certain chance of appearing on each route. We convert that to common/uncommon etc to make it easier.

For newer games like X/Y it will be estimated based on experience playing the game and seeing how many of each Pokemon appear.

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