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Alternative Allele

Definition
AI-generated

The alternative allele (ALT) is any non-reference allele at a site relative to the chosen reference genome.

Topics
Core genetics
Related
Allele Minor Allele Frequency (MAF) Reference Allele

Why it matters in GWAS

PLINK2 and VCF workflows use REF/ALT; ALT frequency is reported instead of MAF in some outputs, so frequency-based and reference-based allele labels must not be conflated.

Example usage

"During harmonization, we verified that the reported effect corresponded to the alternative allele in the target reference build."

Allele Minor Allele Frequency (MAF) Reference Allele Single Nucleotide Polymorphism (SNP)
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

← Alternate contig Alternative Hypothesis →

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