Table 1.

Allele configurations and their expected frequencies.

Allele configuration	Freq. notation	Double non-identity	Expectation			Expectation notation
			$p_A{q}_B$	$p_A{q}_B\left(p_X+q_X\right)$	$p_A{p}_X{q}_B{q}_X$
Digenic
$Z_{B\dots }^{A\dots }$	$P_1$		1			$E_1$
$Z_{\cdot B\dots }^{A\cdot \dots }$	$P_2$		1			$E_2$
$Z_{\cdot \dots \mid B\dots }^{A\dots \mid \cdot \dots }$	$P_3$		1			$E_3$
Trigenic
$Z_{B\cdot \dots }^{AA\dots },Z_{BB\dots }^{A\cdot \dots }$	$P_4$		2	$-P$		$E_4$
$Z_{\cdot \dots \mid B\dots }^{AA\dots \mid \cdot \dots },Z_{BB\dots \mid \cdot \dots }^{\cdot \dots \mid A\dots }$	$P_5$		2	$-P$		$E_5$
$Z_{B\dots \mid \cdot \dots }^{A\dots \mid A\dots },Z_{B\dots \mid B\dots }^{A\dots \mid \cdot \dots }$	$P_6$		2	$-\mathrm{\Pi }$		$E_6$
$Z_{\cdot B\dots \mid \cdot \dots }^{A\cdot \dots \mid A\dots },Z_{\cdot B\dots \mid B\dots }^{A\cdot \dots \mid \cdot \dots }$	$P_7$		2	$-\mathrm{\Pi }$		$E_7$
$Z_{\cdot \dots \mid \cdot \dots \mid B\dots }^{A\dots ∣A\dots ∣\cdot \dots },Z_{\cdot \dots \mid B\dots \mid B\dots }^{A\dots ∣\cdot \dots ∣\cdot \dots }$	$P_8$		2	$-\mathrm{\Pi }$		$E_8$
$Z_{\cdot B\dots }^{AA\cdot \dots },Z_{\cdot BB\dots }^{A\cdot \cdot \dots }$	$P_9$		2	$-P$		$E_9$
Quadgenic
Dihaplotypic
$Z_{BB\dots }^{AA\dots }$	$P_{10}$	${\mathrm{\Theta }}_1$	1	$-P$	${\mathrm{\Theta }}_1$	$E_{10}$
$Z_{B\dots \mid B\dots }^{A\dots \mid A\dots }$	$P_{11}$	${\mathrm{\Theta }}_2$	1	$-\mathrm{\Pi }$	${\mathrm{\Theta }}_2$	$E_{11}$
Trihaplotypic
$Z_{B\dots \mid \cdot B\dots }^{A\dots \mid A\cdot \dots }$	$P_{12}$	${\mathrm{\Gamma }}_1$	1	$-\mathrm{\Pi }$	${\mathrm{\Gamma }}_1$	$E_{12}$
$Z_{B\cdot \dots \mid B\dots }^{AA\dots \mid \cdot \dots },Z_{BB\dots \mid \cdot \dots }^{A\cdot \dots \mid A\dots }$	$P_{13}$	${\mathrm{\Gamma }}_2$	2	$-P-\mathrm{\Pi }$	$2{\mathrm{\Gamma }}_2$	$E_{13}$
$Z_{B\dots \mid \cdot \dots \mid B\dots }^{A\dots \mid A\dots \mid \cdot \dots }$	$P_{14}$	${\mathrm{\Gamma }}_3$	1	$-\mathrm{\Pi }$	${\mathrm{\Gamma }}_3$	$E_{14}$
$Z_{B\cdot B\dots }^{AA\cdot \dots }$	$P_{15}$	${\mathrm{\Gamma }}_4$	1	$-P$	${\mathrm{\Gamma }}_4$	$E_{15}$
Quadhaplotypic
$Z_{\cdot B\dots \mid \cdot B\dots }^{A\cdot \dots \mid A\cdot \dots }$	$P_{16}$	${\mathrm{\Delta }}_1$	1	$-\mathrm{\Pi }$	${\mathrm{\Delta }}_1$	$E_{16}$
$Z_{\cdot \cdot \dots \mid BB\dots }^{AA\dots \mid \cdot \cdot \dots }$	$P_{17}$	${\mathrm{\Delta }}_2$	1	$-P$	${\mathrm{\Delta }}_2$	$E_{17}$
$Z_{\cdot B\dots \mid \cdot \dots \mid B\dots }^{A\cdot \dots \mid A\dots \mid \cdot \dots }$	$P_{18}$	${\mathrm{\Delta }}_3$	1	$-\mathrm{\Pi }$	${\mathrm{\Delta }}_3$	$E_{18}$
$Z_{\cdot \cdot \dots \mid B\dots \mid B\dots }^{AA\dots \mid \cdot \dots \mid \cdot \dots },Z_{BB\dots ∣\cdot \dots ∣\cdot \dots }^{\cdot \cdot \dots \mid A\dots \mid A\dots }$	$P_{19}$	${\mathrm{\Delta }}_4$	2	$-P-\mathrm{\Pi }$	$2{\mathrm{\Delta }}_4$	$E_{19}$
$Z_{\cdot \dots \mid \cdot \dots \mid B\dots \mid B\dots }^{A\dots \mid A\dots \mid \cdot \dots \mid \cdot \dots }$	$P_{20}$	${\mathrm{\Delta }}_5$	1	$-\mathrm{\Pi }$	${\mathrm{\Delta }}_5$	$E_{20}$
$Z_{\cdot \cdot BB\dots }^{AA\cdot \cdot \dots }$	$P_{21}$	${\mathrm{\Delta }}_6$	1	$-P$	${\mathrm{\Delta }}_6$	$E_{21}$
$Z_{\cdot \cdot B\dots \mid B\dots }^{AA\cdot \dots \mid \cdot \dots },Z_{BB\cdot \dots \mid \cdot \dots }^{\cdot \cdot A\dots \mid A\dots }$	$P_{22}$	${\mathrm{\Delta }}_7$	2	$-P-\mathrm{\Pi }$	$2{\mathrm{\Delta }}_7$	$E_{22}$

Z denotes an allele configuration, P and $\mathrm{\Pi }$ denote the single non-identity coefficient within and between individuals. Superscripts and subscripts denote the genotype patterns at two target loci, respectively. The vertical bars separate individuals, · denotes an allele copy in any form, and$\dots$denotes the remaining allele copies. The allele copies in the same position are in the same haplotype. For example, $Z_{B\dots }^{A\dots }$, $Z_{\cdot B\dots }^{A\cdot \dots }$ and $Z_{\cdot \dots \mid B\dots }^{A\dots \mid \cdot \dots }$ denote the two target alleles are in the same haplotype, different haplotypes in the same individual, and different individuals, respectively.