PokéBase - Pokémon Q&A
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Consider the following scenario:
1. I have deposited a Japanese ditto holding destiny knot at the day care.
2. I have a magikarp with hidden ability in party. I save the game and deposit the magikarp.
3. After let's say collecting 'n' number of eggs I get a shiny magikarp with swift swim ability (normal ability).

4.I reload and repeat 2nd and 3rd step but I collect n-1 eggs and reject the nth egg. I collect the next egg (nth egg in box) and that egg contains a shiny magikarp with hidden ability.
5. I reload and deposit a sheer force nidoking holding everstone.

How should I go about collecting egg's to get shiny? And will I get a male or a female nidoran? And will the gender of the shiny magikarp affect the nidoran I hatch?

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This is the best swap breeding guide I know of, but it doesn't say anything about Nidoran. http://i.imgur.com/M7x08pp.png I'm guessing they roll for species the same way other Pokemon roll for gender, so you don't have to worry about rejecting eggs. Remember this is just a guess.
I tested swap breeding of nidoking  with 5 magikarp eggs. In one case, I collected 5 nidoran eggs straight and in another case I rejected the first egg and collected the next 5 alternate eggs. For both cases,   none of the  hatched nidoran eggs had matching  genders or abilities with the 5 magikarps.

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