# remaining human genome variation that hasn't been sequenced?

Given all the genome variation information we have accumulated from resequencing human genomes up until now (early 2018), how much variation is left that hasn't been sequenced?

EDIT: given one of the answers, and the fact that 99% of the SNPs at 1% or more are found, is there a quantitative measure of remaining variation?

• I don't think this is answerable. Do you mean single nucleotide variants? Copy number changes? In healthy individuals only? Only living individuals? All possible variants? Pretty much anything is possible. . . Jan 21 '18 at 23:37
• Please clarify "variation". If you limit this to single nucleotide polymorphisms only and to variants above a certain frequency threshold, as the answer you have received has done, then it might indeed be answerable. Jan 22 '18 at 9:02

The above is a theoretical analysis. In practice, there are two major complications. First, we are not a Wright-Fisher population. Due to recent population expansion, each haplotype harbors more new mutations than the Wright-Fisher model would predict. Given a known population history, it is actually possible to numerically compute $f(x)$, the fraction of variants with frequency below x (for Wright-Fisher, $f(x)=x$). I don't have this result, though. Second, 1000g and many other genome projects didn't call SNPs in repetitive regions and missed a significant portion of high-frequency indels and structural variations. With Illumina, you can only call ~30% of long deletions callable with PacBio data, but we only have a dozen of PacBio human genomes in public. There are still a lot we don't know.