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Deviation of SNPs from the Hardy-Weinberg equilibrium was performed using the chi-square test and the Hardy-Weinberg equilibrium calculator [ 41].
Deviations from Hardy Weinberg proportions were tested for each marker, using the HW equilibrium calculator (http://www.oege.org/software/hwe-mr-calc.shtml) as previously described (Rodriguez et al., 2009).
Finally, to compare the expected genotype frequencies against the observed frequencies, we used a chi-square test applied through the Hardy Weinberg equilibrium calculator, in addition to a Fisher's exact test.
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Online software http://www.had2know.com/academics/hardy-weinberg-equilibrium-calculator-2-alleles.html was used to assess Hardy-Weinberg equilibrium for genotype frequency in controls by a Pearson's goodness-of-fit χ test to compare the observed genotype frequencies to the expected ones, with one degree of freedom.
The distribution of the SNP genotypes was studied using an Excel-based Hardy-Weinberg equilibrium (HWE) calculator [ 20].
Hardy-Weinberg equilibrium was calculated using the Hardy-Weinberg Calculator software as implemented in http://www.tufts.edu.edu
Chi-square Hardy Weinberg equilibrium (HWE) test calculator for biallelic markers available at http://www.oege.org/software/hwe-mr-calc.shtml [7] was used to test for deviations of genotype frequencies from HWE.
Testing for deviation from Hardy-Weinberg equilibrium (HWE) using an HWE calculator was performed, and observed genotype frequencies of the studied polymorphisms were in agreement with HWE (χ = 0.291, P = 0.864 for MnSOD and χ = 0.828, P = 0.363 for GSTM1).
Adjustment for population stratification was made by calculating Hardy Weinberg equilibrium test of single-nucleotide polymorphism (SNP) using Michael H Court's (2005 2008) online calculator 28 and SNPStats.
The He for those loci was also calculated using the Web-based calculator (http://www.genomics.liv.ac.uk/animal/pic.html), assuming Hardy Weinberg equilibrium (HWE).
We tested for Hardy-Weinberg equilibrium (HWE) among controls using a calculator available on the internet [ 13].
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