variance explained by each SNP

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variance explained by each SNP

Postby biancaneve » Fri Jan 20, 2017 8:58 am

I am using the GenABEL package and I have 900 cows genotyped at the HD Illumina SNP panel. 630 thousand markers passed the quality check.
The analyzed phenotype is longevity expressed in days from first calving to culling, mean=1578 ± 665 days.
For each marker I have:
1. Effect of the minor allele
2. Standard error of the effect of the minor allele
3. Frequency of the minor allele
4. Chi2 of the effect
5. P-value of the chi2 of the effect
The variance explained by one SNP should be 2 p q a[2]
Is “a” the effect of the minor allele? Should this effect be standardized? Should it be divided by the average longevity (1578 days)? Or by the standard deviation (665 days)?
Should this effect be squared?
Or maybe is “a” the standard error of the effect of the minor allele?

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