My HiSeq run yielded an average quality score of over Q35, with >90% of the bases being >Q30. Yet, when I analyze these reads, I can read the sequence right off the "nucleotide contributions" plot (this plot shows relative abundance of nucleotides at each base position in the read). Even if it is a faulty library/library prep, this doesn't seem to add up. I would expect the quality to be much poorer due to low diversity. Has anyone ever seen this before?