Measuring sequencing accuracy

Understand quality scores, or Q scores, and what they mean for your sequencing run

Sequencing Quality Scores

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
Sequencing Technology Video

See how Illumina SBS works.

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
Relationship Between Sequencing Quality Score and Base Call Accuracy
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 why PhiX can be used as an in-run control for run quality monitoring in Illumina NGS.

Read Bulletin

For more in-depth information about sequencing quality scores, read the following technical notes:

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