I have a strain of mice (https://www.jax.org/strain/035398) that I am having trouble genotyping. I am following the PCR protocol provided for this strain, where 151 bp and 300 bp are the respective bands for the mutant and WT alleles.

I had previously run a gel with equal amounts of all 4 primers (forward and reverse for both the mutant and WT alleles) in a 20 uL reaction, but this results in a gel that only shows bands for the mutant allele at 151 bp. I then ran a gel with just the WT primers and then got a gel that would only show the WT allele at 300 bp. I also separately tested annealing temperature and cycle amount changes, but these did not affect anything.

Are my primers interfering with each other? If so, which set of primers should I change the amount of? My first instinct is to halve the amount of Mutant primers used in my mastermix, but I wanted to see what others had to say first. I have attached an example of the gels run and the protocol I have been using for mixing amounts for mastermix.

Thank you!