Background information
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 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.”
The IGSR: The International Genome Sample Resource has this entry:
Which reference assembly do you use?
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:
http://www.ncbi.nlm.nih.gov/nuccore/NC_001807.4?report=genbank
The updated Mitochondrial sequence, NC_012920 can be found here: