Quality Scoring

A quality score, or Q-score, is a prediction of the probability of an incorrect base call. A higher Q-score implies that a base call is higher quality and more likely to be correct.

The Q-score is a compact way to communicate small error probabilities. Q(X) represents quality scores, where X is the score. The following table shows the relationship between the quality score and error probability.

Q-score Q(X)	Error Probability
Q40	0.0001 (1 in 10,000)
Q30	0.001 (1 in 1,000)
Q20	0.01 (1 in 100)
Q10	0.1 (1 in 10)

Quality scoring calculates a set of predictors for each base call, and then uses the predictor values to look up the Q-score in a quality table. Quality tables are created to provide optimally accurate quality predictions for runs generated by a specific configuration of sequencing platform and version of chemistry.

After the Q-score is determined, results are recorded in the base call files.