[biophysboy]

I know that the error rate of the oxford nanopore sequencer depends on GC content (guanine/cytosine nucleotides), and that the Pacific Biosciences sequencer uses a polymerase that gets worn down during reading. So there is some non-uniformity in the chemistry.

[ampdepolymerase]

GC rich regions as in hairpin loops? How would the sequencer deal with those?

[biophysboy]

If I'm not mistaken the nanopore tech unwinds double-stranded DNA during the reading, so I don't think hairpins are the issue.