[inciampati]

Actually the level of variation per genome relative to a reference is still not completely known because we do not have more than a handful of truly complete assemblies. It is clear though that it is much higher than a few million base pairs, perhaps as high as tens of millions, depending on your alignment parameters. Most of the differences are in regions we have not been able to sequence and assemble until the past few years. This paper being a key example. If two males have different versions of large repetitive arrays on the Y then they will already be much more than "a few million" base pairs different