Oxford Nanopore mapping Quality and sequencing error
Where i know with the phred score mapQ of 60 means 99.9999% of the bases are called correctly.


That's not at all what the MAPQ means, it means that the sequence is very likely to have originated from that place in the genome, whether the underlying sequence is correct is another question all together.

For long nanopore reads, sequence quality is not well correlated with MAPQ. MAPQ will tend to be either very low (0 or 1) or very high (60) since you tend to have kb+ reads and those will largely be uniquely assignable in the genome. The sequencing quality of nanopore reads is only an issue when you care about something at the base level, such as SNP calling or finding exact splice junctions. Even then, you mostly need sufficient coverage to get around this.