We have modified our version of hg19 to map reads to the revised Cambridge Reference Sequence (rCRS, NC_012920, ) for mitochondrial variants. This is the standard human mtDNA sequence  used in the field and is already included as the mitochondrial genome in hg38. Analysis from user-provided VCF files containing the original hg19 version will also be annotated.
For hg19, we now map mitochondrial variants and transcripts both to chrM (the mitochondrial chromosome in the default hg19) and MT (the rCRS mentioned above). Please read here for more information. We are working on providing support for MitoMap soon.