Sequencing Quality Scores
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.
A quality score of 20 (Q20) represents an error rate of 1 in 100 (meaning every 100 bp sequencing read may contain an error), with a corresponding call accuracy of 99%.
When sequencing quality reaches Q30, virtually all of the reads will be perfect, with no errors or ambiguities. This is why Q30 is considered a benchmark for quality in next-generation sequencing (NGS).
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.
Run Quality Monitoring
Learn what PhiX is and how it can be used as an in-run control for sequencing run quality monitoring in Illumina NGS.
Read BulletinMore About Quality Scores
For more in-depth information about sequencing quality scores, read the following technical notes:
Benefits of SBS Technology
Proven base-calling accuracy and uniform coverage enable robust base calling across the genome, giving you confidence in your results.
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NGS Experimental Design
Learn about read length, coverage, and other experimental considerations to help you plan your sequencing run.
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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