Total number of individuals: 1295

Number of individuals with 0 missing data: 949
Number of individuals with 1 missing data: 346
Number of individuals with 2 missing data: 0
Number of individuals with 3 missing data: 0
Number of individuals with 4 missing data: 0
Number of individuals with 5 missing data: 0
Number of individuals with 6 missing data: 0

Total number of censored individuals: 129
Total number of censored individuals without missing data: 129


Allele frequency at locus 1 (1/2) 0.97945 / 0.02055	p(HWE) = 0.518100
Allele frequency at locus 2 (1/2) 0.93151 / 0.06849	p(HWE) = 0.430948
Allele frequency at locus 3 (1/2) 0.98103 / 0.01897	p(HWE) = 0.551441
Allele frequency at locus 4 (1/2) 0.99631 / 0.00369	p(HWE) = 0.000000
Allele frequency at locus 5 (1/2) 0.97998 / 0.02002	p(HWE) = 0.305307
Allele frequency at locus 6 (2/1) 0.81507 / 0.18493	p(HWE) = 0.583703

Frequencies of Plausible Haplotype under Linkage Equilibrium

Haplotype [0]	111112	0.712293
Haplotype [1]	111111	0.161613
Haplotype [2]	111122	0.014552
Haplotype [3]	111121	0.003302
Haplotype [4]	111212	0.002637
Haplotype [5]	111211	0.000598
Haplotype [6]	111222	0.000054
Haplotype [8]	112112	0.013772
Haplotype [9]	112111	0.003125
Haplotype [10]	112122	0.000281
Haplotype [11]	112121	0.000064
Haplotype [16]	121112	0.052375
Haplotype [17]	121111	0.011883
Haplotype [18]	121122	0.001070
Haplotype [19]	121121	0.000243
Haplotype [24]	122112	0.001013
Haplotype [25]	122111	0.000230
Haplotype [26]	122122	0.000021
Haplotype [27]	122121	0.000005
Haplotype [32]	211112	0.014943
Haplotype [33]	211111	0.003390
Haplotype [48]	221112	0.001099


After 2501 iterations burn at step 1500


Estimated Haplotype Frequencies under Linkage Disequilibrium

				Estimation			

Haplotype 1 [0] 	111112	0.721310
Haplotype 2 [1] 	111111	0.164351
Haplotype 7 [2] 	111122	0.002353
Haplotype 10 [3] 	111121	0.000816
Haplotype 6 [4] 	111212	0.003161
Haplotype 12 [6] 	111222	0.000527
Haplotype 8 [9] 	112111	0.002115
Haplotype 5 [11] 	112121	0.016326
Haplotype 3 [16] 	121112	0.067966
Haplotype 11 [24] 	122112	0.000527
Haplotype 4 [32] 	211112	0.019224
Haplotype 9 [33] 	211111	0.001324


Estimated Haplotype Frequencies in	Uncensored (=0)	Censored (=1) individuals

Haplotype 1 [0] 	111112		0.714976	0.761578
Haplotype 2 [1] 	111111		0.166725	0.149264
Haplotype 7 [2] 	111122		0.002721	0.000012
Haplotype 10 [3] 	111121		0.000944	0.000000
Haplotype 6 [4] 	111212		0.003659	0.000000
Haplotype 12 [6] 	111222		0.000610	0.000000
Haplotype 8 [9] 	112111		0.002446	0.000012
Haplotype 5 [11] 	112121		0.016457	0.015492
Haplotype 3 [16] 	121112		0.069512	0.058140
Haplotype 11 [24] 	122112		0.000610	0.000000
Haplotype 4 [32] 	211112		0.020108	0.013605
Haplotype 9 [33] 	211111		0.001234	0.001899



			Haplotype Effects
				Estimation	StError		T-Test

Intercept 1	111112	
Haplotype 2	111111		-0.12857	0.158657	-0.810368
			HRR = 0.87935 [0.64433 - 1.20009]  p=0.417729

Haplotype 7	111122		0.00000	
Haplotype 10	111121		0.00000	
Haplotype 6	111212		0.00000	
Haplotype 12	111222		0.00000	
Haplotype 8	112111		0.00000	
Haplotype 5	112121		-0.21458	0.515288	-0.416435
			HRR = 0.80688 [0.29389 - 2.21528]  p=0.677092

Haplotype 3	121112		-0.18738	0.258669	-0.724386
			HRR = 0.82913 [0.49939 - 1.37660]  p=0.468829

Haplotype 11	122112		0.00000	
Haplotype 4	211112		-0.42152	0.601697	-0.700554
			HRR = 0.65605 [0.20173 - 2.13359]  p=0.483581

Haplotype 9	211111		0.00000	


-2 x Log-likelihood (with covariates)    = 1701.020546 (Nb studied subjects = 949)
-2 x Log-likelihood (without covariates) = 1702.707953     (df =  4)



Polymorphism 1 1/2
Haplotypic Background -11112	1-4	HRR = 0.65605 [0.20173 - 2.13359]  p=0.483581

Haplotypic Background -11111	2-9	

Polymorphism 2 1/2
Haplotypic Background 1-1112	1-3	HRR = 0.82913 [0.49939 - 1.37660]  p=0.468829


Polymorphism 3 1/2
Haplotypic Background 11-111	2-8	
Haplotypic Background 11-121	10-5	
Haplotypic Background 12-112	3-11	

Polymorphism 4 1/2
Haplotypic Background 111-12	1-6	
Haplotypic Background 111-22	7-12	

Polymorphism 5 1/2
Haplotypic Background 1111-2	1-7	
Haplotypic Background 1111-1	2-10	
Haplotypic Background 1112-2	6-12	
Haplotypic Background 1121-1	8-5	

Polymorphism 6 2/1
Haplotypic Background 11111-	1-2	HRR = 0.87935 [0.64433 - 1.20009]  p=0.417729

Haplotypic Background 11112-	7-10	
Haplotypic Background 21111-	4-9	
