Has anyone looked at the isolates whose phenotype and genotype don't match?

[hollygene]

• genotype: resistant, phenotype, susceptible:
  • is there another mutation that is counteracting the first? gene expr differences?
• genotype: susceptible, phenotype: resistant:
  • is there a new mutation that is conferring resistance?

[hollygene]

Using a k-mer approach could be useful for this - they are able to detect all kinds of variation
Tools:
SEER
Bugwas
PhenotypeSeeker
Kover (reference-free)
PySEER (SEER in python)
HAWK
DBGWAS - bridges gap between k-mers and SNPs