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Revision as of 08:16, 12 December 2014
, 08:16, 12 December 2014→Single Variant Association Analysis
22 36998907 36998907 22:36998907_C/T 62 61 1 0.49194 0.00015557 -3.782 31 31 0.30645 0.67742
22 36998907 36998907 22:36998907_C/T 62 61 1 0.49194 0.00015557 -3.782 31 31 0.30645 0.67742
22 36667082 36667082 22:36667082_T/G 62 28 1 0.22581 0.0003506 -3.5747 31 31 0.080645 0.37097
22 36667082 36667082 22:36667082_T/G 62 28 1 0.22581 0.0003506 -3.5747 31 31 0.080645 0.37097
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Interpretation for top associated variant chr22:36995620_A/G:
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#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE NS.CASE NS.CTRL AF.CASE AF.CTRL
22 36995620 36995620 22:36995620_A/G 62 36 1 0.29032 5.6717e-09 5.8262 31 31 0.51613 0.064516
The score test PVALUE = 5.6717e-09 is strongly significant.
For the notation chr22:36995620_A/G, the reference allele is the first allele "A", and the non-reference (effect) allele is the second allele "G".
The SCORE statistic = 0.29032 is positive (e.g. SCORE>0), meaning that the effect allele INCREASES your risk for disease. Note that the SCORE is NOT the BETA or log odds ratio. To calculate the BETA and SE(BETA), you must run the b.wald test.
There is a large difference between the allele frequencies for cases and controls. AF.CASE = 0.51613 >> AF.CTRL = 0.0064516.
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