Good question. Practically they call their complete sequence a 'reference sequence' which can be thought of as a baseline for comparison to the complete spectrum of human Y chromosome genetic variation, so at least people have something to use as a standard for comparison. The line in the abstract "mapped available population variation, clinical variants" is about the only mention of the issue.
Ideally we'd have hundreds if not thousands of complete genomes which in total would reveal the population diversity of the human species as it currently exists, but this is a big ask. "Clincal variants" are of particular interest as those are regions of the genome associated with certain inherited diseases, although the promises of individual genomic knowledge leading to a medical revolution have turned out to be wildly overblown.
Since the paper is paywalled, there's not much else to say than that they have a (fairly arbitrary in origin, i.e. it could have been from any one individual or possibly even a chimera of several individuals) reference sequence to which other specific human Y chromosomes can be compared, eventually leading to a larger dataset from many individuals which will reveal the highly conserved and highly variable regions of the chromosome, population-wise.
Ideally we'd have hundreds if not thousands of complete genomes which in total would reveal the population diversity of the human species as it currently exists, but this is a big ask. "Clincal variants" are of particular interest as those are regions of the genome associated with certain inherited diseases, although the promises of individual genomic knowledge leading to a medical revolution have turned out to be wildly overblown.
Since the paper is paywalled, there's not much else to say than that they have a (fairly arbitrary in origin, i.e. it could have been from any one individual or possibly even a chimera of several individuals) reference sequence to which other specific human Y chromosomes can be compared, eventually leading to a larger dataset from many individuals which will reveal the highly conserved and highly variable regions of the chromosome, population-wise.