An alternate coloration is a rare color morph of any Pokémon that is not its standard coloration. Pokémon with an alternate coloration are more widely known as being Shiny, but in Pokémon Sardonyx: Raised to Win this extends to Metallic and Shiny Metallic Pokémon. These colors are purely cosmetic and have no effect on stats, moves, or Abilities. Fans have likened alternate colorations to real-world albinism, melanism, and other pigmentation variants seen in animals such as the red fox and peacock.
Pokémon in the canon games may be prevented by the code to never appear Shiny; this is known as Shiny Locking and applies primarily to Legendary and event Pokémon. In Sardonyx, it is only restricted to Mystery Gift and uncatchable wild Pokémon.
Shiny Pokémon are little more than recolors, and give a sparkling sound effect when sent into battle. In Sardonyx, they are marked with an orange star in their summary or HP bar. Shiny Pokémon can vary from their normal colors dramatically (changing all colors completely, such as Charizard going from orange to black) or by only a few shades (such as Pikachu, which becomes slightly darker). However, in Sardonyx, many of these less distinct Shiny Pokémon (or even those generally considered bad by the community) have been changed to more dramatic colorations (for example, Nidoqueen is now purple when Shiny instead of green). Shiny Pokémon have a 1/4096 chance of appearing in any wild encounter; while this rate cannot be improved as of the current Sardonyx build, there are plans to include methods such as the Shiny Charm found in the official games.
Metallic Pokémon are specific to Sardonyx and are a reference to the "monochrome" glitch that occurred in the early weeks of the Generation 6 core series games, Pokémon X and Y. They are marked by a blue-silver icon in their summary and HP bars, opposite of where the Shiny star would appear. Metallic Pokémon are duller in color and much higher in contrast, giving the appearance of having a metal coating. Generally the entire Pokémon is affected, though in some cases (such as Pokémon with open flames as part of their designs) certain parts of the Pokémon may be left untouched or even intentionally over-saturated and brightened. The lore behind Metallic Pokémon is currently unrevealed aside from their rarity. Metallic Pokémon have half the chance of spawning that Shiny Pokémon do, at 1/8192 (the original odds for Shiny Pokémon prior to Generation 6). Unlike Shiny Pokémon, however, there is currently no known way to increase these odds- it has already been confirmed that genetics does not affect it, and thus the "Masuda Method" (breeding two Pokémon of different languages or real-world regions to increase the Shiny chance) does not apply.
Shiny Metallic Pokémon
These two color morphs can combine into what is known as a Shiny Metallic Pokémon. These share the complete recolor of the Shiny variant (though do not share the exact colors involved and are often radically different) and the lustrous, high-contrast sheen of the Metallic variant. As expected, they have both the Shiny and Metallic markings, animations, and sound effects. However, the base chances of a Shiny Metallic Pokémon spawning are abysmally low- as the game's code runs a check for Shiny, then a check for Metallic, the odds are multiplied rather than added. Thus, instead of being a flat 1/12,288 spawn rate, the odds are in fact 1/33,554,432. As it is possible for a Circuit Supplier to provide a guaranteed Shiny or Metallic Pokémon, the easiest method of obtaining a Shiny Metallic is to soft reset for a Shiny on a Pokémon that is guaranteed to be Metallic. However, since the Supplier's selection is limited, this is only possible on certain Pokémon.