Incoming links: Allele
In the case of indel mutations (see limits of gel electrophoresis for minimal size difference issues), it is possible to determine the allele with gel electrophoresis. You can just read out the alleles right in the gel. It is a thing of beauty.
As of 2020, this method appears to be much cheaper than DNA sequencing approaches.
They are actually inheritable! But alleles are rare: www.ncbi.nlm.nih.gov/pmc/articles/PMC5559844
To rats with the same genome differing only in DNA methylation with a different tail phenotype.
Source. 