how long before a fresh chilli pepper is cooked? If I was to add a fresh chilli pepper at the end of cooking, how long in a simmer would you say before its been cooked(all unsafe  things killed and it has released its flavour)?
You can certainly eat fresh chili raw, so no need to worry about killing anything (give it a rinse first).  It depends on the effect you are after.  Typically, "at the end of cooking" means to turn off the heat and add the ingredient.