Phred score (Q score)

Quality value for each sequenced base

The Phred score is a measure for base quality in DNA sequencing. The larger the Phred value, the better the quality of a sequenced base.

Phred Error-rate Accuracy

10 1 of 10 90% # very low quality

20 1 of 100 99% # minimum quality for many tools

30 1 of 1000 99.9% # reasonable good quality

40 1 of 10000 99.99% # high quality

50 1 of 100000 99.999% # very high quality

Quality Score Encoding

example quality string in fastq files (ASCII 33 Encoding)

%&?@AB

corresponding Phred quality scores

4 5 30 32 33

→ Illumina quality codes

read more

https://en.wikipedia.org/wiki/FASTQ_format

https://en.wikipedia.org/wiki/Phred_quality_score

https://www.illumina.com/documents/products/technotes/technote_Q-Scores.pdf