The idea of sequence quality scores can be traced back to the original description of the SCF file  format by 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.
However, early attempts to develop base-specific quality scores had only limited success.
The first program to develop accurate and powerful base-specific quality scores was the program Phred. Phred was able to calculate highly accurate quality scores that were logarithmically linked to the error probabilities. Phred was quickly adopted by all the major genome sequencing centers as well as many other laboratories; the vast majority of the DNA sequences produced during the Human Genome Project were processed with Phred.
After Phred quality scores became the required standard in DNA sequencing, other manufacturers of DNA sequencing instruments, including Li-Cor and ABI, developed similar quality scoring metrics for their base calling software.