******Results of the Case-control Association tests ******

There are 300 individuals from 1 independent families. 117 of the individuals are affected, 183 of the individuals are unaffected, and 0 of the individuals are of unknown phenotype.

The prevalence value used in the MQLS calculations is 0.200000 

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Analysis of Marker 1 

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There are 117 affected individuals, 183 unaffected individuals, and 0 individuals of unknown phenotype available. 

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MQLS test using robust variance estimate

MQLS statistic value  = 0.170939	 pvalue = 0.679279  df = 1


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Case-control corrected chi-squared test using robust variance estimate 

Corrected chi-squared statistic value = 1.259410	 pvalue = 0.261763  df = 1 

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WQLS test using robust variance estimate 

WQLS statistic value = 2.431405	 pvalue = 0.118926  df = 1


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allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in 
			 cases 			 controls 			 all sample 
allele 1 : freq = 0.1714  sd = 0.0792	 freq = 0.2057  sd = 0.0815		 freq = 0.1740  sd = 0.0749
allele 2 : freq = 0.8286  sd = 0.0792	 freq = 0.7943  sd = 0.0815		 freq = 0.8260  sd = 0.0749
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allele frequency estimates using naive counting in
		 cases 		 controls 		  all sample 
allele 1 : freq = 0.1795	 freq = 0.2322		 freq = 0.2117
allele 2 : freq = 0.8205	 freq = 0.7678		 freq = 0.7883
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Analysis of Marker 2 

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There are 117 affected individuals, 183 unaffected individuals, and 0 individuals of unknown phenotype available. 

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MQLS test using robust variance estimate

MQLS statistic value  = 5.971756	 pvalue = 0.112992  df = 3


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Case-control corrected chi-squared test using robust variance estimate 

Corrected chi-squared statistic value = 3.339997	 pvalue = 0.342114  df = 3 

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WQLS test using robust variance estimate 

WQLS statistic value = 2.675224	 pvalue = 0.444454  df = 3


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allele frequency estimates using the Best Linear Unbiased Estimator (BLUE) in 
			 cases 			 controls 			 all sample 
allele 1 : freq = 0.0580  sd = 0.0491	 freq = 0.1356  sd = 0.0690		 freq = 0.1179  sd = 0.0638
allele 2 : freq = 0.2391  sd = 0.0896	 freq = 0.2423  sd = 0.0864		 freq = 0.2414  sd = 0.0846
allele 3 : freq = 0.2882  sd = 0.0952	 freq = 0.2469  sd = 0.0869		 freq = 0.2493  sd = 0.0855
allele 4 : freq = 0.4147  sd = 0.1035	 freq = 0.3753  sd = 0.0976		 freq = 0.3913  sd = 0.0965
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allele frequency estimates using naive counting in
		 cases 		 controls 		  all sample 
allele 1 : freq = 0.0427	 freq = 0.0984		 freq = 0.0767
allele 2 : freq = 0.2949	 freq = 0.2951		 freq = 0.2950
allele 3 : freq = 0.2991	 freq = 0.2322		 freq = 0.2583
allele 4 : freq = 0.3632	 freq = 0.3743		 freq = 0.3700
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