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?