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Are you using the 1000 genomes build of GR37? There is another post about 5 questions down from this one in the list labelled "HG19 genome" that references the mitochondrial genome in the 1000 genomes version. We are using that build and have no problems with visualizing the mitochondrial region of the BAM file (Samtools output shows chrM as chromosome for our files, if that is helpful)
