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Several options for Ditto to hide as do not share the same normal typing. Therefore, it's possible to see, for example, a Seedot that is weather boosted during sunny weather, and when caught it turns out to be a Ditto that would not have been weather boosted.

How is level/IVs/stardust calculated for this catch, is it weather boosted or no?

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According to The Silph Road (no really, I googled this and it was the #1 result):

  1. You get stardust/exp for the pokemon you caught being weather boosted. eg. if it is Partly Cloudy you'll get a boost catching Ditto (but not if it is Sunny and the Ditto is disguised as Seedot).
    • The disguise will still show the weather-boost icon
  2. Levels and IVs are not affected.

Because Levels and IV aren't affected, if is possible to come across a pokemon that is weather boosted, but its CP is below the minimum possible for a weather boosted pokemon of that type (revealing itself to be a Ditto or other pokemon in disguise before it is captured).

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  • I accepted this for the stellar link (thank you for finding that) but your summary doesn't seem to match what the link says. The link says you only get 100 stardust, not a weather-boosted 125. – Kadima Dec 30 '19 at 17:24
  • @Kadima Maybe I'm misreading, but this was the part I saw, The dust will change to base 80 and it'll get +20 "weather boost" if the disguised pokemon is weather boosted, resulting in the normal 100 dust. But the Partly Cloudy will weather boost 100 +25. That seemed to indicate a boost, but I'll admit that it's slightly contradictory. – Draco18s no longer trusts SE Dec 30 '19 at 17:54
  • I think it's saying that if the disguise is boosted you'll get 80+20, but if the Ditto itself would be boosted because of its normal typing in Partly Cloudy weather, then you'll get boosted to 125. – Kadima Dec 30 '19 at 17:58
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    Edited the post to fix a typo and hopefully clarify based on that. – Draco18s no longer trusts SE Dec 30 '19 at 18:17
  • The summary screen shows 80+20 for normal catch, which caught my eye. At the time, I searched around for this because it was unusual, and one report suggested it was a bug workaround to give you 100 total stardust though unrelated to weather boost. Since then, I have caught a couple more Ditto with the same result. Have you ever gotten 125 stardust for Ditto? – Jerry Dec 30 '19 at 22:38

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