What is a Quality Score in Sequencing?
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.
Sequencing Technology Video
See how Illumina SBS works.
Q Score Definition
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.
- Higher Q scores indicate a smaller probability of error.
- Lower Q scores can result in a significant portion of the reads being unusable. They may also lead to increased false-positive variant calls, resulting in inaccurate conclusions.
As shown below, a quality score of 20 represents an error rate of 1 in 100, with a corresponding call accuracy of 99%.
SBS Technology Overview
Illumina technology enables massively parallel sequencing with optimized SBS chemistry.
Learn More| 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 Quality Scores
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 BulletinAdditional Information About Quality Scores
For more in-depth information about sequencing quality scores, read the following technical notes:
Beginner's Guide to NGS
Considering bringing NGS to your lab, but unsure where to start? These resources cover key topics in NGS and are designed to help you plan your first experiment.
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References
- Ewing B, Hillier L, Wendl MC, Green P. (1998): Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8(3):175-185
- Ewing B, Green P. (1998): Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8(3):186-194