Heterozygosity - HW
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A Report with allele Heterozygosity and results of a Hardy-Weinberg test sorted by SNP can be generated here. The Report is sent to the User Results section.

The columns in the Report stand for:

SNP     
Code of SNP

N
Number of Genotypes (results)  for this SNP.

H. Observed
Observed Heterozygosity. (Heterozygous genotypes / total genotypes)

H. Expected
Expected Heterozygosity calculated from the allele frequency.

Chi-squared
Calculated from a table of two cells (Heterozygous / Homozygous). This has been calculated this way to keep working when more than two alleles are present in a SNP.

There may be differences with results obtained from other softwares which use a table with 3 cells (AA / AB / BB).

P
P-value obtained from the Chi-square above using 1 degree of freedom.

Validity
Not valid (N) when there is some expected value in the chi-squared contingency table that is equal or below 1.

- Batch mode.


This is a fundamental time-saving feature. Selecting one of the fields in the Samples or SNP table, SNPator will run this analysis as many times as different values are in that fields, using each time only those samples or SNPs that have each of the values. For instance, if you have defined your samples in the "sex" field as "M" or "W", selecting "sex" as the attribute of the Sample batch mode will result in having two runs of the analysis, taking separately men and women.

If you select at the same time sample and SNP batch fields, you are going to obtain as many runs of the analysis as all possible combinations of the values of samples and SNPs in the fields you selected.

- Haploid data treatment:

Currently, only diploid genotypes are supported. Those SNPs containing haploid genotypes will be excluded from the calculation and a warning indication will appear in the results file.