We use the Cambridge Reference Sequence (rCRS) for chromosome M with the GenBank accession number NC_012920. UCSC has announced that they also are using this version in the next human assembly release.

The following background information is from the UCSC site http://genome.ucsc.edu/cgi-bin/hgGateway?org=human&db=hg19

"Note on chrMSince the release of the UCSC hg19 assembly, the Homo sapiens mitochondrion sequence (represented as 'chrM' in the Genome Browser) has been replaced in GenBank with the record NC_012920. We have not replaced the original sequence, NC_001807 in the hg19 Genome Browser. We plan to use the Revised Cambridge Reference Sequence (rCRS) in the next human assembly release."