Maybe someone can explain what exactly it means. Are all the variants of every allele now mapped? Of course everyone might have a slightly different variant, so what does it mean?
What does complete mean?
What does complete mean?
One common analogy is to consider the genome sequence (a.k.a. assembly) as a map. Since the initial publication of the human genome in the early 2000s, most regions of human DNA has been known in full resolution. Other portions, most prominently the repetitive centromeres that lie at the middle of chromosomes, have remained unmapped. It was known that they exist, approximately how big they were, and which types of sequences lay inside, but the full order of the sequence had never been determined for any human genome until this work.
You could consider the genome like the earth and the centromeres like a dense rainforest. Previously we had detailed maps of most of the earth, and we had mapped the boundaries of the rainforest and had satellite-level images (i.e. we knew they were full of plants). Now we have on-the-ground pictures with full detail.
Having a map of these sequences makes the accessible to study. One of the most valuable uses of the human genome is as a shared coordinate system used by scientists to compare different individuals and identify and name genetic variants that explain human traits. We lacked that coordinate system for a big chunk of the genome until now.
As you say, this paper reports the sequence of a single human cell line named CHM13. Each of us has a slightly different genome sequence (really two of them, one from each parent). Now when scientists sequence the genomes of more individuals, they can look at these regions that were previously ignored. Certainly understanding those regions will improve our understanding of human biology. Exactly how much will remain to be seen.
* Telomerase is a reverse transcriptase that allows to achieve replicative immortality (https://academic.oup.com/hmg/article/9/3/403/715108).
Mitochondria have their own DNA, which is also sequenced.
So, this complete genome is a full set of 23 sequences without any "not sure" positions or "gaps" in the sequence.
With new techniques you generate much longer pieces, so there is much less confusion.
"However, limitations of BAC cloning led to an underrepresentation of repetitive sequences, and the opportunistic assembly of BACs derived from multiple individuals resulted in a mosaic of haplotypes. As a result, several GRC assembly gaps are unsolvable because of incompatible structural polymorphisms on their flanks, and many other repetitive and polymorphic regions were left unfinished or incorrectly assembled (5)."
Looks like there were "gaps" in the sequence due to technical limitations associated with the original sequencing methods and the authors have filled in those gaps. I haven't read the full paper, though.
Every human has unique de novo germline mutations (estimated to be in the range of 100 to 200).
In addition every cell (other than RBCs) will have a small number of its own unique somatic mutations.
And then there is radiation!