Interpreting LoFreq output quality score
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3.5 years ago
jleehan ▴ 110

The output for LoFreq provides a quality score for each SNP that it calls. However this quality score does not appear to be a typical Phred value score that would max out at 40. I'm seeing values that range from ~50 to 49,314. I am assuming as 49,314 is a high value as expected SNPs are receiving this assignment, however I would like to know exactly how to interpret the quality value that LoFreq provides so that I can better establish a quality threshold for noise.

Do any of you know how to interpret the quality score in LoFreq output?

Thanks!

lofreq SNP next-gen sequencing • 986 views
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