Mutation
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Mutations act much like traits, in that they give your character a variety of passive effects. Unlike traits, which can be selected upon creating a new character, mutations can only be obtained in-game and are somewhat random. Like traits, mutations can be both beneficial and harmful to your character.
Does it hurt?
Yeah, sometimes. Mutations can be obtained by consuming some questionable products (mutagens, misshapen fetuses, arms, legs, sewage samples), romping through radioactive areas, and other unhealthy methods. There is 2/3 chance to have any mutation and 1/3 chance to have only a "bad" mutation, though not all "bad" mutations are really bad ones and not all "good" mutations are equally desirable. Also, check Robust Genetics trait, which changes chances drastically. It flips the 1/3 chance to have only a "bad" mutation to a 1/3 chance to have only a "good" mutation.
If you end up with unwanted mutations a purifier can help purge them. It will revert up to four mutations (this chance is higher if you have a lot of mutations). Note, that purifier will not remove a trait that you took upon character creation or decrease strength of mutation category!
Even if there is no forced "bad" mutation, chances are not equal for all traits. Mutations are split up into a dozen categories and even more trees. Trees have various requirements for the different branches and most branches being opposed to one another. The more branches are opened up, the less likely a new branch or a categorized mutation will be gained, with the game prioritizing current upgrades to everything else. Direct upgrades have the most priority, with a (5/(number of available upgrades + 5)) chance to be skipped, then mutations from a category pool, and only then game picks random mutations from the full list of all mutations.
Trait will be gained if any of its evolutions are picked and lost when opposed or rival trait are chosen.
Categories
Traits tend to provoke other mutations from the same category.
Every time, when mutation occurs, "strongest" category with the most numerous current mutations is chosen. There is a (strength/total_strength) chance that a random mutation will be chosen from this category. If it fails this test (due to amount of traits-outsiders), or there are no more mutations in the category, then a random mutation is selected, without any linkage to categories at all. Every in-category trait gives 8 points to his category strength. Every not-in-category trait takes away one point from each rival category unless that category already has strength 0 or passes a 1/strength check.
Once a mutation is selected, you will begin to mutate towards it. If any mutations you currently have conflict with this mutation, then one of the conflicting mutations is randomly removed. If you have no conflicting mutations, but don't have any of the prerequisites, you will begin to mutate towards a random prerequisite. If you already have a prerequisite mutation and no conflicting mutations, you gain the selected mutation immediately.
Starting traits are underlined. However, initial traits do not increase respective categories strength, unless you gain them later via actual mutation! On the upside, this does mean that you can take Robust Genetics without placing yourself into the rather undesirable slime category.
For a complete list of mutations click here