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Ploidy & Special Chromosomes

AFQuery computes ploidy-aware AN for sex chromosomes (chrX, chrY) and the mitochondrial chromosome (chrM). This ensures that allele frequencies are correct when querying these chromosomes, where the number of alleles per sample differs from the diploid autosomes.

Chromosome name normalization

AFQuery accepts MT, chrMT, and chrM as input; output always uses chrM.

Ploidy Rules

Chromosome Female AN contribution Male AN contribution
Autosomes (chr1–22) 2 2
chrX (non-PAR) 2 1
chrX (PAR1, PAR2) 2 2
chrY 0 1
chrM 1 1

For each eligible sample at a given position, AFQuery adds the appropriate ploidy count to AN based on the sample's sex and the chromosome/position.

Pseudoautosomal Regions (PAR)

The pseudoautosomal regions on chrX and chrY behave like autosomes — both males and females contribute AN=2 on chrX PAR. PAR coordinates by genome build:

GRCh38

chrX:

Region Start End
PAR1 10,001 2,781,479
PAR2 155,701,383 156,030,895

chrY:

Region Start End
PAR1 10,001 2,781,479
PAR2 56,887,903 57,217,415

GRCh37 / hg19

chrX:

Region Start End
PAR1 60,001 2,699,520
PAR2 154,931,044 155,260,560

chrY:

Region Start End
PAR1 10,001 2,649,520
PAR2 59,034,050 59,363,566

Positions within PAR1 or PAR2 on chrX are treated as diploid for all samples.

Effect on AF Queries

chrY

Querying chrY with --sex female returns AN=0 (females have no Y chromosome):

afquery query --db ./db/ --locus chrY:2787758 --sex female
# chrY:2787758 — no results (AN=0 for all variants)

afquery query --db ./db/ --locus chrY:2787758 --sex male
# chrY:2787758 C>T  AC=3  AN=856  AF=0.0035  n_eligible=856  N_HET=0  N_HOM_ALT=3  N_HOM_REF=853  N_FAIL=0

chrX non-PAR

Male samples contribute AN=1, female samples contribute AN=2. This means a cohort of 500 females and 500 males has AN = 500×2 + 500×1 = 1500 at a non-PAR X position.

afquery query --db ./db/ --locus chrX:100000000
# N_total = 1000 samples, AN = 1500 (not 2000)

chrM

All samples are haploid at mitochondrial loci:

afquery query --db ./db/ --locus chrM:3243
# AN = n_samples (one allele per sample)

Genotype Counting

Counting Identity

For every query result, the following identity holds:

N_HET + N_HOM_ALT + N_HOM_REF + N_FAIL = n_eligible

This can be used to validate results. N_HOM_REF is the number of eligible samples that are homozygous reference (i.e., do not carry the alt allele and passed quality filters).

Mutual exclusivity

N_HET, N_HOM_ALT, N_HOM_REF, and N_FAIL are mutually exclusive. A sample with a non-ref allele but FILTER≠PASS is counted in N_FAIL only — it does not appear in N_HET or N_HOM_ALT. Likewise, N_HOM_REF counts only PASS-filtered samples.

chrX non-PAR

  • A male with GT=1 contributes AC=1, AN=1
  • A female with GT=0/1 contributes AC=1, AN=2
  • A female with GT=1/1 contributes AC=2, AN=2

N_HET and N_HOM_ALT are counted per sample (not per allele):

  • Males at chrX non-PAR (haploid positions) are counted in N_HOM_ALT when GT=1, because all alleles at that position are alternate. N_HET is reserved for diploid positions where both reference and alternate alleles are present.
  • Females at chrX with GT=0/1 are counted in N_HET; with GT=1/1 in N_HOM_ALT.

chrY

chrY is fully haploid (males only, females contribute AN=0):

  • All carriers are counted in N_HOM_ALT (never N_HET)
  • N_HET is always 0 on chrY

chrM

chrM is haploid for all samples (both sexes contribute AN=1):

  • All carriers are counted in N_HOM_ALT (never N_HET)
  • N_HET is always 0 on chrM

N_HET is always 0 on haploid regions

On chrY, chrM, and chrX non-PAR for males, all carriers are counted in N_HOM_ALT. N_HET is 0 because haploid samples have only one allele copy — there is no heterozygous state. This is correct behavior, not a bug.

Sex Filter Interaction

When --sex female is used on chrX (non-PAR), AN is purely diploid:

  • Each eligible female contributes AN=2
  • AF is computed over a fully diploid denominator

When --sex male is used on chrX (non-PAR), AN is purely haploid:

  • Each eligible male contributes AN=1
  • AF reflects the observed allele frequency in haploid male calls

This makes it straightforward to compare X-linked variant frequencies between sexes without manual ploidy adjustment.

Next Steps