HW-QuickCheck

Software for checking genotypes for agreement with Hardy-Weinberg expectations

 

 

Introduction

There are many programs for comparing genotypes with Hardy-Weinberg expectations. HW-QuickCheck may be the simplest. You paste a list a genotypes into a textbox and HW-QuickCheck tests the genotypes for equilibrium using a nice set of exact tests. It is designed to be used early in the genotyping process so that allelic dropout and null alleles can be detected as soon as possible.

Instructions for use

Paste a lists of genotypes genotypes into the textbox labeled 'Input' and then click 'Check." Genotypes may be in one of three formats.

1. Tab delimited; each allele separated by a tab. This format is compatible with pasting genotypes from a spreadsheet.

2. Space delimited; each allele separated by a space.

3. GENEPOP format (either 4 or 6 digits).

 

Documentation

The statistical tests performed by HW-QuickCheck are described in the manuscript below:

Kalinowski ST (In review) HW-QuickCheck: an easy-to-use computer program for checking genotypes for agreement with Hardy-Weinberg expectations. Molecular Ecology Notes.

 

 

System Requirements

HW-QuickCheck runs on the Microsoft Windows operating system that has the .NET platform installed. See my Software page for instructions on how to install this on your computer (it may already be there).

Right-click here to download  HW-QuickCheck.

 

 

Installation / UnInstallation

Click on HW-QuickCheck.exe to run. Delete HW-QuickCheck.exe to "uninstall."

 

 

User Interface

The user interface for HW-QuickCheck looks like this:

 

Sample Output

Here is a sample output from the program.

 

SUMMARY

Sample size: 59

N alleles:   6

Hobs:        0.64

Hexp:        0.78

 

ALLELE FREQUENCIES

138    0.01 <-- Singleton

146    0.08

148    0.26

150    0.29

152    0.23

154    0.13

 

GLOBAL TEST     OBS    EXP    SIGN   P VALUE

Homozygotes     21     13.1   >

Heterozygotes   38     45.9   <

                                     0.0101

 

HOMOZYGOTES     OBS    EXP    SIGN   P VALUE

138/138         0      0.0    =      ns

146/146         1      0.4    +      ns

148/148         5      4.0    +      ns

150/150         6      4.8    +      ns

152/152         7      3.0    +      0.006

154/154         2      0.9    +      ns

 

HETEROZYGOTES   OBS    EXP    SIGN   P VALUE

138/146         0      0.1    -      ns

138/148         0      0.3    -      ns

138/150         1      0.3    +      ns

138/152         0      0.2    -      ns

138/154         0      0.1    -      ns

146/148         3      2.6    +      ns

146/150         2      2.9    -      ns

146/152         1      2.3    -      ns

146/154         2      1.3    +      ns

148/150         10     9.0    +      ns

148/152         5      7.2    -      ns

148/154         3      4.0    -      ns

150/152         5      7.8    -      ns

150/154         4      4.4    -      ns

152/154         2      3.5    -      ns

 

 

NOTES

 

1. P-values reported above are for one tailed tests.

   For example, if there is an excess of homozygotes,

   the P-value is the one tailed probability of observing this number

   (or more) homozygotes (conditional on the alleles counts observed

   in the sample). If there is a deficiency of homozygotes, the P-value

   is the one tailed probability of observing this few homozgyotes.

 

2. P-value for two tailed tests can be obtained by doubling the

   P-values reported here.

 

3. 'ns' indicates that a P value is > 0.10.

 

4. Only complete genotypes are included in the analysis. Genotypes missing

   data for one allele are not included.

 

5. The P-value for the global test is obtained via a randomization test,

   and, therefore, will be slightly different each time it is calculated.

   All the other P-values are calculated analytically.

 

 

 

 

 

 

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