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Low-complexity region (LCR)

Definition
AI-generated

A low-complexity region (LCR) is genomic sequence with skewed base composition or abundant tandem or near-tandem repeats, so that k-mer entropy is low and aligners or assemblers may place reads ambiguously.

Topics
Sequencing Data Analysis
Synonyms
LCR
Related
Blacklisted region Homopolymer Mappability

Why it matters in GWAS

LCRs overlap many genes and regulatory intervals; miscalls or missing genotypes in these intervals can distort fine-mapping, burden masks, and rare-variant QC, so pipelines often flag or exclude them alongside homopolymers and mappability tracks.

Example usage

"We masked low-complexity region (LCR) intervals before indel validation in repetitive exons."

Blacklisted region Homopolymer Mappability Short-read sequencing Variant Calling
Related-term network

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References

  • Wootton JC, Federhen S. (1996). Analysis of compositionally biased regions in sequence databases. Methods Enzymol.
  • Treangen TJ, Salzberg SL. (2011). Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet.
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