Several types of overall marker statistics and genetic measures may be output.

NOTE: These statistics will only be output for bi-allelic markers.

NOTE: If there is a case/control dependent variable, or a dependent variable that is being treated as case/control, several of these statistics will not only be output for all samples, but will also be output separately for cases and for controls.

NOTE: These statistics may be output without running any association tests. To do so, see 18.10.

18.7.1 Minor Allele Frequency

This option displays the fraction of the total alleles of the given marker that are minor alleles.

18.7.2 Output Spreadsheet of DD/Dd/dd genotypes

This option produces an additional spreadsheet output where the bi-allelic genotypes are coded as minor allele homozygous (DD), heterozygous (Dd) and major allele homozygous (dd) for each genetic column.

This is useful as it gives insight into whether the genotypic tests view a specific sample as having two minor alleles (DD), one minor allele (Dd) or no minor alleles (dd).

18.7.3 Call Rate

This option displays the fraction of genotypes that are present and not missing for the given marker.

18.7.4 Hardy-Weinberg Equilibrium P-Value

This option displays the HWE Correlation P-Values for each marker.

This statistic is the same as that computed for the HWE display, which is computed as documented in 15.1.12.

This statistic will also be output separately for cases and for controls, if applicable.

18.7.5 Fisher’s Exact Test for HWE P-Value

This option displays Fisher’s Exact Test HWE P-Values for each marker.

This statistic will also be output separately for cases and for controls, if applicable.

See Section 26.24.1 in the Formulas and Theories chapter for an explanation of this statistic.

18.7.6 Signed HWE R

This option displays the Signed HWE Correlation R for each marker. This is a measure designed to show specifically if the data for this marker shows a tendency towards being homozygous (positive signed R) or towards being heterozygous (negative signed R).

This statistic will also be output separately for cases and for controls, if applicable.

See Section 26.24.2 in the Formulas and Theories chapter for an explanation of this statistic.

18.7.7 Genotype Count Table(s)

The numbers of samples that contain each genotype are output. These will also be output separately for cases and for controls, if applicable.

18.7.8 Allele Count Table(s)

The counts for each allele are output. These will also be output separately for cases and for controls, if applicable.