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Read mapping

Definition
AI-generated

Read mapping (read alignment) places short or long sequencing reads on a reference genome, yielding position, orientation, and base-level agreement or disagreement with the reference.

Topics
Sequencing Data Analysis
Synonyms
Read alignment
Related
Mapping quality (MAPQ) Read Reference genome

Why it matters in GWAS

Mapping errors create false SNVs and indels or miss real variants; WGS association pipelines spend substantial effort on mapper choice, duplicate marking, and MAPQ-aware filtering.

Example usage

"Read mapping with BWA-MEM preceded variant calling; unmapped and low-MAPQ reads were excluded."

Mapping quality (MAPQ) Read Reference genome Soft clipping
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References

  • Li H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv.
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