R (Rhaegar Targaryen) + L (Lyanna Stark) = J (Jon Snow, or possibly Jaehaerys Targaryen).
Jon Snow isn't the bastard son of Ned Stark. And, in case there was any doubt, Jon Snow's father is definitely Rhaegar Targaryen. HBO low-key confirmed that fact with a handy infographic published in a "Game of Thrones" blog post shortly after "The Winds of Winter" aired.
Now, though, it appears we didn't have to wait for that scene of Lyanna Stark giving birth to know Jon Snow pretty much has the most legitimate claim to the Iron Throne. Apparently, "A Song of Ice and Fire" author George RR Martin told us back in 2002 about Jon's real parents.
To which Martin apparently replied,
Combine that response with the Tower of Joy scene and what we know now and, well, Martin basically answered one of the biggest "GoT" questions we've ever had 14 years ago.
And, as DeadHopesAndDreams points out, there's also the fact Martin used "Ned" instead of "father" when addressing Snow's parentage. A small, but very important detail.