Indel variation in reference alleles lead to sporadic ST miscalls for S. aureus

[keyfm]

Hi,
I am studying within-person S.aureus variability, and sequence many isolates to characterize the population diversity.

I observe sporadically ST inconsistencies, where single isolates are called NF while other isolates get a ST assigned, despite phylogenetic confirmation of genetically close relationships on the genome level.

Inspection of the alignment identifies the miscalled allele carries a deletion (in the middle of the gene) compared to the presumable correct allele (in the attached screenshot the deletion is at position 114). How can I correct that behavior?

Thanks!
felix