Phred-like Score Characteristics
- Estimates a probability of error for each base-call, as a function of certain parameters computed from the trace data.
- These error probabilities are to validate base-calls – increase the confidence to discriminate correct base-calls from incorrect ones
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The quality value q assigned to a base-call: q = -10 × log10(p) where p is the estimated error probability for that base-call.
Parameter 1: Peak Spacing
- The ratio of the largest peak-to-peak spacing, in a window of seven peaks centered on the current one, to the smallest peak-to-peak spacing. The minimum possible value of one corresponds to evenly spaced peaks.
Parameter 2: Uncalled/Called Ratio 7
- The ratio of the amplitude of the largest uncalled peak, in a window of seven peaks around the current one, to the smallest called peak.
Parameter 3: Uncalled/Called Ratio 3
- Same as parameter 2, but using a window of three peaks.
Parameter 4: Peak Resolution
- The number of bases between the current base and the nearest unresolved base, times -1 (to force the parameter to have the right direction).
The Lookup Table
- There is a lookup table consisting of a set of lines, each line containing a set of parameter thresholds, together with the quality value (score) corresponding to those thresholds.
Set the Phred-like Score
- Search the lookup table, to find the lines where each corresponding parameter is bigger than the base’s, then select the highest score in the lines.