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Old 01-28-2010, 10:33 AM   #1
maggie
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Default QV scores

What does a QV>=30 mean exactly? How do the quality scores from one platform relate to the quality scores from another platform? Thanks.
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Old 01-28-2010, 10:44 AM   #2
maubp
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Quality values are generally PHRED scores, given as a base 10 log transform of the probability of error at that base. A PHRED score of 30 means the chance of a miscall is estimated at 1 in 1000. See:
http://en.wikipedia.org/wiki/Phred_quality_score

Different platforms have different underlying error properties, and different ways to estimate them.

Note Solexa/Illumina used to use their own (alternative) log transform, but as of 1.3 of their pipeline they now use PHRED scores.

Last edited by maubp; 01-28-2010 at 10:45 AM. Reason: Added link
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