Phreds

Phreds is a term used in genomics to refer to Phred quality scores, which quantify the probability that a base call in a DNA sequencing read is incorrect. The scores arise from the Phred software suite, developed in the late 1980s for base calling and quality assessment of Sanger sequencing data. In practice, each nucleotide in a read is assigned a Phred score that reflects its estimated error probability; higher scores indicate higher confidence.

Technical basis and encoding: quality scores are logarithmic: Q = -10 log10 P, where P is the probability of an incorrect base call. A score of 20 corresponds to a 1% error rate, 30 to 0.1%, and so on. Phred quality values are commonly stored alongside sequence data in FASTQ files, in which the score is represented as ASCII characters.

Applications and impact: Phred scores are used to filter low-quality bases and trim reads, improving the reliability of downstream analyses such as assembly, mapping, and variant calling. The Phred-Phrap-Consed ecosystem, originally including the Phred program for base-calling, Phrap for assembly, and Consed for viewing and editing, played a central role in early high-throughput sequencing projects and helped standardize data quality assessment. Today, the term Phreds is often used informally to refer to quality scores and their role in quality control, though the original software has largely been superseded by newer pipelines.