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Alternate contig

Definition
AI-generated

Alternate contigs (ALT contigs) are additional sequences in a reference assembly representing divergent haplotypes or unplaced scaffolds; reads may map to primary chromosomes or ALTs.

Topics
Sequencing Data Analysis
Synonyms
ALT contig
Related
Contig Reference genome

Why it matters in GWAS

ALT-aware mapping changes coordinate systems and variant representation; mismatched reference bundles break harmonization.

Example usage

"The pipeline indexed alternate contig sequences in the GRCh38 full analysis set."

Contig Reference genome
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

  • Schneider VA, et al. (2017). Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res.
← Alpha helix Alternative Allele →

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