Quality Scores
Bérénice Batut
Natalie Kucher
Helena RascheBut what does this quality score mean?
The quality score for each sequence is a string of characters, one for each base of the nucleotide sequence, used to characterize the probability of misidentification of each base. The score is encoded using the ASCII character table (with some historical differences):
To save space, the sequencer records an ASCII character to represent scores 0-42. For example 10 corresponds to “+” and 40 corresponds to “I”. FastQC knows how to translate this. This is often called “Phred” scoring.
So there is an ASCII character associated with each nucleotide, representing its Phred quality score, the probability of an incorrect base call:
| Phred Quality Score | Probability of incorrect base call | Base call accuracy |
|---|---|---|
| 10 | 1 in 10 | 90% |
| 20 | 1 in 100 | 99% |
| 30 | 1 in 1000 | 99.9% |
| 40 | 1 in 10,000 | 99.99% |
| 50 | 1 in 100,000 | 99.999% |
| 60 | 1 in 1,000,000 | 99.9999% |
What does 0-42 represent? These numbers, when plugged into a formula, tell us the probability of an error for that base. This is the formula, where Q is our quality score (0-42) and P is the probability of an error:
Q = -10 log10(P)
Using this formula, we can calculate that a quality score of 40 means only 0.00010 probability of an error!