The biggest misconception is that Google indexes websites. Google does NOT index websites. Repeat after me, Google does NOT index websites.
What? Yes that's right, Google does not index websites. Google only index web pages. There's a huge difference between a website and many web pages.
Website -> All the web pages and how they relate to each others.
Webpage -> One single webpage, independently of any other webpage on your website
Google may have indexed only a couple of page from your website and still be ranked very highly.