Quality Scores

Quality scores measure the probability that a base is called incorrectly. With 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 quality score of a given base, Q, is defined by the equation
Q = -10log10(e)

where e is the estimated probability of the base call being wrong. Thus, a higher quality score indicates a smaller probability of error. In the table below, a quality score of 20 represents an error rate of 1 in 100, with a corresponding call accuracy of 99%.

The Relationship Between 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%

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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