A Phred score is a quality score used to indicate the accuracy of nucleotide base calls in sequencing data. It is calculated based on the probability of an incorrect base call, with higher scores indicating greater confidence. The score is represented on a logarithmic scale, where a Phred score of 20 corresponds to a 1 in 100 chance of an error, while a score of 30 corresponds to a 1 in 1,000 chance. Phred scores are included in FASTQ files as part of the quality string and are essential for evaluating the reliability of sequencing reads before alignment and variant calling.