FUT2 secretor inference report

secretor_status is the inferred phenotype (secretor, weak-secretor, or non-secretor). unknown means the method could not assign a status. Default --phenotype-coding biochemical reports Se^w/Se^w and Se^w/se as weak-secretor. --phenotype-coding gwas recodes those diplotypes as non-secretor. fut2_genotype is the diplotype (for example Se/se) and always keeps Se^w; ambiguous means more than one diplotype was compatible with the unphased genotypes. Population percentages are informational only; samples are never rejected for frequency deviation.

genoSecretor fetches only FUT2 tag SNPs (rs601338, rs1047781, rs602662) from the input file. Variants are matched by rsID, contig and position (including chr-prefixed and RefSeq contig aliases), then by allele-aware keys.

Genome build is resolved from marker coordinates, file-header metadata, and contig lengths, or taken from an explicit --build setting. Conflicting evidence is an error; the build is never guessed silently.

Per-sample genotypes are interpreted from hardcalls (GT), dosage (DS), or genotype probabilities (GP) according to the selected genotype mode. REF/ALT alleles are then mapped to biological marker states. Inference rules never operate on raw VCF alleles.

The selected method applies haplotype and diplotype rules and emits secretor_status, fut2_genotype, confidence, and QC fields.

Ancestry-aware 2-marker inference (rs601338 + rs1047781)

Markers: rs601338, rs1047781

Method was auto-selected: rs601338 and rs1047781 available

• Markers: rs601338 (complete LoF se428 / W143X) and rs1047781 (weak se385 / I129F).
• A haplotype with rs601338 LOF is se. Otherwise rs1047781 WEAK yields Se^w and FUNCTIONAL yields Se.
• Phenotype is recessive: se/se is non-secretor; Se^w/Se^w and Se^w/se are weak-secretor under --phenotype-coding biochemical (default) or non-secretor under gwas; any Se haplotype is secretor.
• When both markers are heterozygous and unphased, --assume-trans (default) assigns Se^w/se; --no-assume-trans leaves the call ambiguous (Se^w/se or Se/se with both variants in cis).

Research use only. Genotype-inferred FUT2 secretor status does not capture all rare, weak, or otherwise atypical FUT2 alleles and must not be used for clinical decision-making, transfusion, or infection-risk counselling.

• Common secretor inference uses three SNP markers and six common diplotypes under standard assumptions. Rare FUT2 nulls, fusions, and regulatory alleles may be misclassified as functional Se.
• rs1047781 T/T is reported as weak-secretor under --phenotype-coding biochemical (default; reduced FUT2 activity). Pass --phenotype-coding gwas to recode Se^w/Se^w and Se^w/se as non-secretor (Smyth 2011; BBJ-style binary coding). The diplotype column always preserves Se^w.
• rs602662 is an LD proxy for se428, not a functional variant. When it is used, confidence is capped at low. The proxy is not a substitute for rs1047781 in East Asian data.
• The default --assume-trans rule (unphased double-het → Se^w/se) is an ancestral-haplotype assumption. Pass --no-assume-trans to mark those samples ambiguous.
• Low imputation INFO, missing genotypes, and uncertain dosages propagate to low-confidence or unknown calls.
• genoSecretor has not been validated against salivary ABH serology across ancestries. Outputs are intended for population-genetics, epidemiology, GWAS, PheWAS, and biobank research. FUT3/Lewis typing is out of scope.
• Rare FUT2 nulls other than se428 and se385 are not modelled and may be misclassified as Se.
• The default --assume-trans rule (compound heterozygote in trans) is an ancestral-haplotype assumption: se428 and se385 are typically mutually exclusive across continents. Pass --no-assume-trans to leave those samples ambiguous.

Secretor phenotype is inferred from biological marker states after REF/ALT normalization, not from raw VCF alleles. The selected method of this run is named below; unused markers are shown for reference.

This run used method two-marker with markers rs601338, rs1047781.