An "official" comment on this
  http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19
with some more info in this discussion

https://groups.google.com/a/soe.ucsc.edu/forum/?fromgroups=#!topic/genome/hFp-dGG9gBs

Essentially it seems the b37 has been "patched" and this patched release is
not reflected in hg19 but may be (I don't know) reflected in the b37
download from NCBI

Kasper


On Thu, Apr 25, 2013 at 9:49 AM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> I agree with Vincent.  I have seen code from Herve in a package with some
> standardization of chromosome names, and this code could perhaps be used
> more widely so we don't have all the problems with chr1 vs chr01 vs 1.
>
> However, in this particular case, if Ulrich is actually interested in the
> mitochondrial genome, he has a problem.
>
> hg19, which is the genome version from UCSC is consider equal to NCBIs
> b37.  However, as far as I understand, UCSC screwed up with the
> mitochondrial genome and used an old version for their hg19.  So the error
> message is in many ways right here: the two genomes are slightly different
> because they have different mitochondrial genomes.
>
> Kasper
>

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