Sequencing Quality Scores

Sequencing quality scores measure the probability that a base is called incorrectly. With SBS (sequencing by synthesis) 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.

Introduction to Q Scores

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%.

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 Quality Scores

Illumina sequencing chemistry delivers unparalleled 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.

Additional Information about Quality Scores

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

References

  1. 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
  2. Ewing B, Green P. (1998): Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8(3):186-194

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