How are high phred scores represented?
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2.3 years ago

I have a fastq file with consensus sequences that max out at J (QV=41, which is ASCII 74) . When papers refer to high consensus accuracies with QV's like 60 or 70, what symbols are used to represent these? Will we ever be able to see them in fastq files? If not, how do we know they're QV=60?

consensus assembly • 390 views
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2.3 years ago
colindaven ★ 3.3k

Have a look at the coloured encoding figure at the bottom here: https://en.wikipedia.org/wiki/FASTQ_format

It looks like these characters will be used to encode PHRED scores over 40 ijklmnopqrstuvwxyz{|}~

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In practice, would we ever see these characters in a fastq file?

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Good question. I haven't seen them yet.

Perhaps on a) assemblers which produce highly accurate assemblies (which also produce base quality estimates) or b) corrected long reads with high accuracy eg via the new Pacbio (hifi?) approach or ONTs forthcoming multipore approach with R9.4 and R10 combined ?

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