Originally posted by GenoMax
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Our machine self-reports 87% of bases as having quality above 30, and therefore Illumina claims it is in-spec, but the true quality as measured by mapping for the highest-rated bases (claimed Q37) is only Q28, and the majority are much lower. In other words, bases the machine assigns Q37 are wrong 0.16% of the time rather than the claimed 0.02%, so their quality values are inflated by a factor of 8. In reality, 0% of the output is at least Q30, either from our machine or from Illumina's official PhiX data, which I used because they calibrate their machines on PhiX so it should represent the best case scenario.
Does anyone have a different experience?
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