Table 2 Investigating HWE for two X chromosome SNPs

From: A test for deviations from expected genotype frequencies on the X chromosome for sex-biased admixed populations

SNP

AA

AB

BB

A

B

p f

p m

HWE

LTRA

LRTP

p f,g

p m,g

E-AA

E-AB

E-BB

E-A

E-B

1

27

22

0

42

5

0.78

0.89

0.04

0.06

0.008

0.92

0.6

27.0

20.4

1.6

43.2

3.8

2

17

30

2

38

9

0.65

0.81

0.01

0.12

0.005

0.85

0.42

17.5

27.2

4.3

40.0

7.1

  1. For each SNP, we provide genotype counts in females (AA, AB, and BB) and males (A, B) in the ACB 1000 Genomes population, allele frequencies in females and males (pf and pm, respectively), the P-value for a deviation from HWE in females (χ2 test), and the P-values from our LRTA test and the LRTP test. The rightmost seven columns provide information on the null hypothesis of our LRTA test. Specifically, pf,g and pm,g are the maximum-likelihood estimates of the female and male allele frequencies in the previous generation, respectively. The rightmost five columns are the expected genotype counts in females (E-AA, E-AB, and E-BB) and males (E-A, E-B) under random mating, given the allele frequencies in the previous generation (compare with the actual genotype counts in columns 2–6)
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