I worked with Nanopore data about four years ago, and I found that that's mostly true, but for some reason at some sites, there was systematic errors where more than half of reads were wrong.
I can't 100% prove it wasn't a legit mutation but our lab did several tests where we sequenced the same sample with both Illumina and Nanopore, and found Nanopore to be less than perfect even with exteme depth. Like, out depth was so high we routinely experienced overflow bugs in the assembly software because it stored the depth in a UInt16.
What was the DNA source? At the same time (4 years ago) there were issues with specific species -
Birds and some metagenome species were the worst if I remember correctly.
I can't 100% prove it wasn't a legit mutation but our lab did several tests where we sequenced the same sample with both Illumina and Nanopore, and found Nanopore to be less than perfect even with exteme depth. Like, out depth was so high we routinely experienced overflow bugs in the assembly software because it stored the depth in a UInt16.