Related Experiment Video
Updated: Jan 8, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
Published on: February 3, 2023
Challenges in structural variant calling in low-complexity regions
1Division of Rheumatology, Inflammation and Immunity, Brigham Women's Hospital, Boston, MA 02115, USA.
Background:
Structural variants (SVs) are genomic differences $\ge$50 bp in length. They remain challenging to detect, even with long-sequence reads, and the sources of these difficulties are not well quantified.
Results:
We identified 35.4 Mb of low-complexity regions (LCRs) in GRCh38. Although these regions cover only 1.2% of the genome, they contain 69.1% of confident SVs in sample HG002. Across long-read SV callers, 77.3-91.3% of erroneous SV calls occur within LCRs, with error rates increasing with LCR length.
Conclusion:
SVs are enriched and difficult to call in LCRs. Special care needs to be taken for calling and analyzing these variants.
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