sumwun is right. Based on my experience, I think a good way to clarify it is that that number is not saying every 4,096th Pokemon you encounter will be shiny -- that is just the rough chances of it happening for when you encounter it. In other words, that's the standard chance for you getting a shiny in an individual encounter, not in a grand total. 1/4,096 is the same as 0.0244140625% (so less than a 1% chance of a Pokemon being shiny when you encounter it).