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Mapping quality (MAPQ)

Definition
AI-generated

Mapping quality (MAPQ) is a Phred-scaled score summarizing confidence that a read is placed at its reported location versus alternative mappings; MAPQ 0 often indicates multi-mapping ambiguity.

Topics
Sequencing Data Analysis
Related
Mappability Phred quality score Read mapping

Why it matters in GWAS

Filtering on MAPQ reduces false calls in repeats and segmental duplications where misalignment can mimic variation.

Example usage

"Variants supported only by MAPQ <20 reads were flagged for manual review."

Mappability Phred quality score Read mapping
Related-term network

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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

  • Li H, et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics.
← Mappability Marginal likelihood →

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