Sequencing quality scores measure the probability that a base is called incorrectly. With sequencing by synthesis (SBS) technology, each base in a read is assigned a quality score by a phred-like algorithm1,2, similar to that originally developed for Sanger sequencing experiments.
The sequencing quality score of a given base, Q, is defined by the following equation:
Q = -10log10(e)
where e is the estimated probability of the base call being wrong.
As shown below, a quality score of 20 represents an error rate of 1 in 100, with a corresponding call accuracy of 99%.
|Quality Score||Probability of Incorrect Base Call||Inferred Base Call Accuracy|
|10 (Q10)||1 in 10||90%|
|20 (Q20)||1 in 100||99%|
|30 (Q30)||1 in 1000||99.9%|
Illumina sequencing chemistry delivers high accuracy, with a vast majority of bases scoring Q30 and above. This level of accuracy is ideal for a range of sequencing applications, including clinical research.
Learn how PhiX can be used as an in-run control for run quality monitoring in Illumina NGS.Read PhiX Technical Bulletin
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For more in-depth information about sequencing quality scores, read the following technical notes:
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