The UCSC website has this note about chrM:
“Note on chrM:
Since 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 notreplaced 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.”
The IGSR: The International Genome Sample Resource has this entry:
The reference assembly the 1000 genomes project has mapped sequence data that has changed over the course of the project.
For the pilot phase we mapped data to NCBI36. A copy of our reference fasta file can be found on the ftp site.
For the phase1 and phase 3 analysis we mapped to GRCh37. Our fasta file which can be found here called human_g1k_v37.fasta.gz, it contains the autosomes, X, Y and MT but no haplotype sequence or EBV.
Other links related to chrM:
Original sequence, NC_001807:
The updated Mitochondrial sequence, NC_012920 can be found here: