I'm analyzing some Oxford Nanopore sequencing reads, with several articles stating the sequencing error is between 5% and 15%. Since its 1D and not 1D^2 sequencing i would assume the sequencing error is closer to 15%.
I'm using Minimap2 aligner to align the reads to the reference genome, and then im choosing those reads with a mapQ of 60, to analyze.
Where i know with the phred score mapQ of 60 means 99.9999% of the bases are called correctly.
So my question is, if the mapQ is 60, then does it really matter if my sequencing error is 15%? Or how is the sequencing error correlated with mapQ? Becuase i guess you could still obtain a good mapping quality with a few mismatches?
Or am i completely off target.
Thanks for your time and help.