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Base quality

Definition
AI-generated

Base quality scores encode per-base error probabilities from the sequencer, usually as Phred-scaled Q scores in FASTQ.

Topics
Sequencing Data Analysis
Related
Base Quality Score Recalibration (BQSR) Genotype likelihood Phred quality score

Why it matters in GWAS

Systematic base-quality issues (for example by cycle) can bias allele and indel calls; recalibration steps are common in production pipelines.

Example usage

"Base quality recalibration was applied after duplicate marking and before variant discovery."

Base Quality Score Recalibration (BQSR) Genotype likelihood Phred quality score Sequencing artifact
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Ewing B, Green P. (1998). Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res.
← Base Pair (bp) Base Quality Score Recalibration (BQSR) →

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