TIL that. I was 100% sure the DNA was completely sequenced. Even have a friend with a sequencing company. It is incredible how ignorant one can be. Thank you 10g1k and HN.
Imagine it like putting together a jigsaw puzzle, except that the picture on the front of the puzzle has lots of repeating motifs, so you end up with multiple pieces that look identical. You won't be able to tell how the whole thing fits together, but you can assemble the bits that are well-behaved and unique.
Modern technology gives us larger jigsaw pieces, which allows us to distinguish between almost-identical parts of the puzzle better. But I would note that the project linked did a huge amount of sequencing using very expensive methods to be able to resolve the whole thing.
Modern sequencing techniques allow us o read 200 to 500 bases at a time. So after hat we need do find a way o arrange these short sequences into a single sequence. And this can be prety hard, especially when you are doing 'de novo' assembly[0].
Besides that, there is the fact that some regions of DNA are repeated[1].
[0] - https://en.wikipedia.org/wiki/Third-generation_sequencing#De...
My knowledge cut-off period in this domain is around 2018. So it's not suprising that things moved on.
Because the sequencing uses short reads, it will not be able to resolve parts of the genome that are repetitive with a repeat unit longer than ~150bp. You'll have all the jigsaw pieces from the puzzle, but you won't be able to reconstruct some parts of the picture. Long read sequencing can help with those, but that's more expensive.
Does that mean that every possible polymorphism is accounted for?
Does that mean that 100% of possible polymorphic sites are known?
What about weird edge cases. You have a tandem repeat that is known, but in some small population of humans, there's two tandem repeats with an island of something else in there.