Phred Quality Score (Q)
Definition
A logarithmic probability score for base-call accuracy. Q30 = 99.9% accuracy (1 in 1000 error probability). Q20 = 99% accuracy. Most forensic MPS pipelines apply a Q30 minimum threshold.
- Q30
- 99.9% accuracy, 1 in 1000 error probability
- Q20
- 99% accuracy, 1 in 100 error probability
- Common pipeline threshold
- Q30 minimum
- Applies to
- Per-base call accuracy in MPS/NGS data
Common questions
How is this Q30 threshold actually applied in an MPS pipeline?+
Base calls below the Q30 threshold are typically flagged or filtered out before variant or allele calling proceeds, so low-confidence positions do not get reported as genuine sequence data. The threshold is applied per base, not to the whole read.
Why is a stricter threshold used in massively parallel sequencing than in older Sanger work?+
MPS platforms generate millions of short reads per run, so even a small per-base error rate can produce many false variant calls across a whole dataset. Applying a strict Q30 filter keeps the false-positive rate in variant calling manageable at that scale.
Related terms
- BAM File
- Binary Alignment/Map format, the compressed binary version of a SAM file. Stores aligned reads with their mapping positions, quality scores, and alignment...
- FASTQ
- The standard sequencing output file format containing four-line records per read: identifier, nucleotide sequence, separator, and Phred quality score string. All MPS...
- Isoallele
- Two STR alleles that share the same repeat count (and therefore appear as the same allele on CE) but differ by a...
- Stutter (MPS)
- In MPS, stutter includes both length-based stutter (as in CE, an n-1 repeat artefact from PCR slippage) and sequence-based stutter (single-nucleotide errors...
- VCF
- Variant Call Format, the standard output from variant callers (GATK, FreeBayes). Records each variant position with reference allele, alternative allele(s), genotype likelihoods,...