A Phred quality score is a measure of the quality of the identification of the nucleobases generated by automated DNA sequencing. It was originally developed for the computer program Phred to help in the automation of DNA sequencing in the Human Genome Project. Phred quality scores are assigned to each nucleotide base call in automated sequencer traces. The FASTQ format encodes phred scores as ASCII characters alongside the read sequences. Phred quality scores have become widely accepted to characterize the quality of DNA sequences, and can be used to compare the efficacy of different sequencing methods. Perhaps the most important use of Phred quality scores is the automatic determination of accurate, quality-based consensus sequences.

Phred quality scores ${\displaystyle Q}$ are logarithmically related to the base-calling error probabilities ${\displaystyle P}$ and defined as

${\displaystyle Q=-10\ \log _{10}P}$.

This relation can also be written as

${\displaystyle P=10^{\frac {-Q}{10}}}$.

For example, if Phred assigns a quality score of 30 to a base, the chances that this base is called incorrectly are 1 in 1000.

The phred quality score is the negative ratio of the error probability to the reference level of ${\displaystyle P=1}$ expressed in Decibel (dB).

The idea of sequence quality scores can be traced back to the original description of the SCF file format by Rodger Staden's group in 1992. In 1995, Bonfield and Staden proposed a method to use base-specific quality scores to improve the accuracy of consensus sequences in DNA sequencing projects.