Counts   Called genotypes     Homozygous wild Heterozygous Homozygous variant Observed Nº of XA/XA + Nº of XA/Y Nº of XA/Xa Nº of Xa/Xa+Nº of Xa/Y Expected       2 df [(1−MAF)2P♀+ 2(1−MAF)( MAF) [(MAF)2P♀+MAFP♂]   (1−MAF)P♂]N P♀N N 1 df {[(1−MAF)2+(1− (1−MAF)( MAF)N {[(MAF)2+MAF]0.5} N   MAF)]0.5}N     df: Degrees of freedom N: Number of non-missing observations for the particular SNP Nº: Number; MAF: Minor allele (Xa) frequency in the sample P♀: Prevalence of females in the sample P♂: Prevalence of males in the sample

Table 2: Calculating observed and expected counts for Chi-squared HWE tests with 1 and 2 degrees of freedom