Why do I Get both "000000" and "NullNull" in my ouput files?

This occurs when you have samples in your exported genotype file that have data for some loci but not others.

For example, if you have imported data for sample A genotyped at locus H51, but all other sample data are for loci H51 and H52, you will see results for sample A at H51, but you will receive "NullNull" for sample A's H52 genotype (because the data for sample A at H52 were never imported or have been deleted from the project).

Can GeneMapper handle multiple genotypes at the same locus for the same individual?

The short answer to this question is 'Not really'. When a sample possesses multiple allele values at a particular locus, the last set of allele scores with a GQ score ≥ 0.75 in the exported data file will become the genotype for the individual at a particular, multiply genotyped locus.

If you are comparing scores between multiple genotyping runs for the same individual(s) (e.g. checking genotyping error), it is best to export these as separate data files and convert them separately (e.g. put these sample files in a new project before binning and exporting).