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Old 12-11-2014, 07:34 AM   #17
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Location: Purdue University, West Lafayette, Indiana

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Sorry, no NextSeq data to discuss. But on the issue of quality values vs. empirical error rate -- always seemed to me this would highly depend on the alignment engine and the parameters used. Specifically how gaps (indels) were handled.
A single indel in a read results in nearly all the bases downstream of that indel being scored as "mismatch" unless a gap is introduced into the alignment.

Seems like how gaps are handled could easily explain what Illumina (and I) would call a Q37 base showing up as only Q30 in your analysis. Depending on how you did your alignments...

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