How on earth do you plan to tell whether any particular story did or didn't start out in the author's mind as fanfiction?
Genre =/= quality.
No, genre =/= quality, true. However, I have several ebooks on my computer now that I can tell from within the first thirty pages or so they were fanfic. And, funnily enough, in a fandom I was familiar with because I recognized a few of the fanon conventions frequent in fanfiction of the fandom. I asked for opinion from friends who have read them and with careful questioning, have said the same thing.
Being the curious sort, I did some research and discovered I was right.
In many cases, you can tell. There's a certain cadence, a certain rhythm to the story structure, to the character descriptions, to the prose that marks them as fanfiction. A dependence on certain fanon qualifications that marks the characters as identifiable for fanfic use in an AU.
I dunno, there's just this 'feel' to a fanfiction-originated book as a whole that 'pings' on my fanfiction radar.
I'm sure there are many books out there that were originally fanfiction AUs but don't read that way. I think it's a testament to the writer's skill for them to pull that off.
If the reader doesn't read fanfiction? They may never notice the difference and they may never care. It's fresh and new to them. In a way, I envy that. My long years in fandom, in reading and writing fanfiction has jaded my ability to simply enjoy something when it starts ticking off the markers of fanfiction in my head.
eta: This was dropped on me by a friend. There is a little discussion about fanfiction in general in there that says it better than I did/can.