What it does

The user supplies the following:

1. A optional file in gd_genotype or gd_snp format giving the mitochondrial SNPs.
2. An optional gd_genotype file gives the sequence coverage for each individual at each mitochondrial position.
3. The minimum depth of sequence coverage. Positions where an individual has less coverage are ignoried.
4. A set of individuals specified with the "Specify individuals" tool.
5. A file of annotation for the reference mitochondrial sequence.

The program draws a picture indicating the locations of SNPs and the inadequately covered interval.