After generating the genotype files for the Diversity Outbred Lung (DOL) group for Jacco Boon*, there were issues with GEMMA and R/qtl mapping.
These issues seem to have been caused by a couple mitochondrial markers having a position of 0Mb. For now, I've addressed this by changing their positions to 0.000001 and 0.000002Mb respectively.
There's also an issue that hasn't been addressed yet with displaying mitochondrial markers in the GN2 figure. GEMMA is outputting the results, so I suspect this is because mitochondria isn't included in the databased list of chromosomes associated with Mouse.