------------------------------------------------------------------------------- Program pseudomarker 1.0.6b -- 2011 (C) 2000-2011 Tero Hiekkalinna, Petri Norrgrann and Joseph D. Terwilliger Program for Joint Linkage and/or Linkage Disequilibrium analysis If you find a bug, send email to: tero.hiekkalinna@helsinki.fi ------------------------------------------------------------------------------- Date : Tue Nov 15 13:46:10 2011 Original articles: Linkage Analysis in the Presence of Errors IV: Joint Pseudomarker Analysis of Linkage and/or Linkage Disequilibrium on a Mixture of Pedigrees and Singletons When the Mode of Inheritance Cannot Be Accurately Specified. Harald H. H. Goring and Joseph D. Terwilliger (Am. J. Hum. Genet. 66:1310-1327, 2000). PSEUDOMARKER: A Powerful Program for Joint Linkage and/or Linkage Disequilibrium Analysis on Mixtures of Singletons and Related Individuals. T. Hiekkalinna, A. A. Schäffer, B. W. Lambert, P. Norrgrann, H.H.H. Göring, J.D. Terwilliger. Hum Hered 2011;71:256-266. Input files ======================== Pedigree file : mixed.ped # pedigrees : 205 # persons : 1015 Linkage locus file : mixed.dat Map file : mixed.map Parameters used model-based analysis: =============================================================== Disease allele frequency: P(D) = 0.01 Liability class P(Affected|++) P(Affected|D+) P(Affected|DD) --------------------------------------------------------------- 1 0.01 0.9 0.9 =============================================================== LOD SCORE statistics ==================== Dominant (Phenotype: DISEASE_LOCUS) Marker Linkage SNP1 0.041615 SNP2 5.316922 SNP3 5.739484 STR1 0.077618 STR2 6.956333 STR3 9.747656 Recessive (Phenotype: DISEASE_LOCUS) Marker Linkage SNP1 0.223044 SNP2 1.210150 SNP3 5.099877 STR1 0.052639 STR2 3.510388 STR3 5.590726 Model-based (Phenotype: DISEASE_LOCUS) Marker Linkage SNP1 0.099738 SNP2 5.316309 SNP3 6.491548 STR1 0.076828 STR2 7.724878 STR3 10.939468 p-value statistics ================== Dominant (Phenotype: DISEASE_LOCUS) Marker Linkage LD|Linkage LD|NoLinkage Linkage|LD LD+Linkage SNP1 0.330786 0.782981 0.726543 0.703190 0.739917 SNP2 3.812674e-07 0.216318 0.625973 3.908910e-07 0.000001 SNP3 1.392988e-07 2.877274e-09 0.006054 1.877506e-13 2.154081e-14 STR1 0.274975 0.719843 0.666758 0.651347 0.699834 STR2 7.762360e-09 0.314906 0.827796 5.753830e-09 1.011943e-07 STR3 1.079931e-11 1.616351e-19 0.020290 1.095678e-28 1.477013e-28 Recessive (Phenotype: DISEASE_LOCUS) Marker Linkage LD|Linkage LD|NoLinkage Linkage|LD LD+Linkage SNP1 0.155407 0.927194 0.944336 0.309997 0.452358 SNP2 0.009131 0.053836 0.026676 0.036423 0.005958 SNP3 6.401566e-07 0.000002 0.007135 5.051727e-10 5.861033e-11 STR1 0.311246 0.844112 0.791397 0.736268 0.824227 STR2 0.000029 0.614732 0.975988 0.000036 0.000426 STR3 1.985011e-07 8.109951e-20 0.000021 8.620222e-22 9.975074e-25 Model-based (Phenotype: DISEASE_LOCUS) Marker Linkage LD|Linkage LD|NoLinkage Linkage|LD LD+Linkage SNP1 0.248981 0.246655 0.310990 0.378688 0.292913 SNP2 3.818256e-07 0.103369 0.263620 3.693763e-07 7.374891e-07 SNP3 2.334183e-08 4.033468e-09 0.003761 7.000027e-14 5.289874e-15 STR1 0.275994 0.822344 0.781951 0.614943 0.775791 STR2 1.262375e-09 0.322808 0.946570 8.387814e-10 1.836306e-08 STR3 6.595516e-13 2.289524e-31 2.316665e-09 0.000000e+00 5.879940e-29 -2ln(Likelihood) difference =========================== After -2ln(Like) difference in brackets is the degrees of freedom (df) Dominant (Phenotype: DISEASE_LOCUS) H0 vs. H1 H1 vs. H3 H0 vs. H2 H2 vs. H3 H0 vs. H3 Marker Linkage LD|Linkage LD|NoLinkage Linkage|LD LD+Linkage SNP1 0.191645 (1) 0.075865 (1) 0.122320 (1) 0.145190 (1) 0.267510 (50%:2 50%:1) SNP2 24.485331 (1) 1.528498 (1) 0.237592 (1) 25.776237 (1) 26.013829 (50%:2 50%:1) SNP3 26.431298 (1) 35.319382 (1) 7.538777 (1) 54.211904 (1) 61.750680 (50%:2 50%:1) STR1 0.357445 (1) 0.657443 (2) 0.810656 (2) 0.204232 (1) 1.014888 (50%:3 50%:2) STR2 32.035095 (1) 2.310960 (2) 0.377977 (2) 33.968079 (1) 34.346055 (50%:3 50%:2) STR3 44.889613 (1) 86.537891 (2) 7.795212 (2) 123.632292 (1) 131.427504 (50%:3 50%:2) Recessive (Phenotype: DISEASE_LOCUS) H0 vs. H1 H1 vs. H3 H0 vs. H2 H2 vs. H3 H0 vs. H3 Marker Linkage LD|Linkage LD|NoLinkage Linkage|LD LD+Linkage SNP1 1.027156 (1) 0.008345 (1) 0.004872 (1) 1.030629 (1) 1.035501 (50%:2 50%:1) SNP2 5.572949 (1) 3.718215 (1) 4.913051 (1) 4.378112 (1) 9.291164 (50%:2 50%:1) SNP3 23.485802 (1) 22.473962 (1) 7.242819 (1) 38.716946 (1) 45.959765 (50%:2 50%:1) STR1 0.242413 (1) 0.338941 (2) 0.467912 (2) 0.113442 (1) 0.581354 (50%:3 50%:2) STR2 16.165936 (1) 0.973138 (2) 0.048609 (2) 17.090465 (1) 17.139074 (50%:3 50%:2) STR3 25.746243 (1) 87.917220 (2) 21.525914 (2) 92.137549 (1) 113.663463 (50%:3 50%:2) Model-based (Phenotype: DISEASE_LOCUS) H0 vs. H1 H1 vs. H3 H0 vs. H2 H2 vs. H3 H0 vs. H3 Marker Linkage LD|Linkage LD|NoLinkage Linkage|LD LD+Linkage SNP1 0.459312 (1) 1.342040 (1) 1.026405 (1) 0.774946 (1) 1.801351 (50%:2 50%:1) SNP2 24.482508 (1) 2.652743 (1) 1.249545 (1) 25.885705 (1) 27.135250 (50%:2 50%:1) SNP3 29.894683 (1) 34.660585 (1) 8.401510 (1) 56.153758 (1) 64.555268 (50%:2 50%:1) STR1 0.353805 (1) 0.391192 (2) 0.491925 (2) 0.253072 (1) 0.744997 (50%:3 50%:2) STR2 35.574377 (1) 2.261396 (2) 0.109820 (2) 37.725953 (1) 37.835773 (50%:3 50%:2) STR3 50.378114 (1) 141.103588 (2) 39.766274 (2) 151.715427 (1) 191.481701 (50%:3 50%:2) -2ln(Likelihood) ================ Dominant (Phenotype: DISEASE_LOCUS) Marker H0 H1 H2 H3 SNP1 5107.735617 5107.543972 5107.613298 5107.468107 SNP2 5131.054445 5106.569114 5130.816853 5105.040617 SNP3 5067.184932 5040.753634 5059.646156 5005.434252 STR1 6080.868678 6080.511233 6080.058022 6079.853790 STR2 6074.683109 6042.648013 6074.305132 6040.337054 STR3 5799.721580 5754.831967 5791.926368 5668.294076 Recessive (Phenotype: DISEASE_LOCUS) Marker H0 H1 H2 H3 SNP1 9631.741431 9630.714275 9631.736559 9630.705930 SNP2 9655.060259 9649.487310 9650.147208 9645.769095 SNP3 9591.190746 9567.704943 9583.947927 9545.230981 STR1 10604.874492 10604.632079 10604.406580 10604.293138 STR2 10598.688922 10582.522986 10598.640313 10581.549848 STR3 10323.727393 10297.981150 10302.201479 10210.063930 Model-based (Phenotype: DISEASE_LOCUS) Marker H0 H1 H2 H3 SNP1 4275.067325 4274.608014 4274.040920 4273.265974 SNP2 4298.386154 4273.903646 4297.136608 4271.250904 SNP3 4234.516640 4204.621957 4226.115130 4169.961372 STR1 5248.200386 5247.846582 5247.708461 5247.455389 STR2 5242.014817 5206.440440 5241.904997 5204.179044 STR3 4967.053288 4916.675175 4927.287014 4775.571587 Maximized allele and haplotype frequencies ========================================== Dominant (Phenotype: DISEASE_LOCUS) Marker : SNP1 1 2 Alleles 0.489375 0.510625 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.489375 0.510625 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.388437 0.496250 0.503750 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.460000 0.540000 (D) 0.494375 0.505625 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.395624 0.468125 0.531875 (D) Marker : SNP2 1 2 Alleles 0.523125 0.476875 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.523643 0.476357 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.143828 0.510156 0.489844 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.579883 0.420117 (D) 0.506250 0.493750 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.145117 0.593500 0.406500 (D) Marker : SNP3 1 2 Alleles 0.361875 0.638125 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.361875 0.638125 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.139063 0.296865 0.703135 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.636298 0.363702 (D) 0.291850 0.708150 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.140625 0.656058 0.343942 (D) Marker : STR1 1 2 3 Alleles 0.325625 0.335000 0.339375 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.325625 0.335000 0.339375 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.398750 0.345000 0.316250 0.338750 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.242500 0.415625 0.341875 (D) 0.340625 0.315625 0.343750 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.418125 0.262500 0.417500 0.320000 (D) Marker : STR2 1 2 3 Alleles 0.321875 0.331875 0.346250 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.321875 0.331875 0.346250 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.180938 0.312500 0.325000 0.362500 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.360000 0.360625 0.279375 (D) 0.326875 0.313125 0.360000 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.179687 0.297500 0.410625 0.291875 (D) Marker : STR3 1 2 3 Alleles 0.192875 0.212500 0.594625 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.192875 0.212500 0.594625 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.160312 0.125375 0.214375 0.660250 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.476625 0.207500 0.315875 (D) 0.103500 0.213750 0.682750 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.163125 0.568500 0.208750 0.222750 (D) Recessive (Phenotype: DISEASE_LOCUS) Marker : SNP1 1 2 Alleles 0.489375 0.510625 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.489375 0.510625 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.377812 0.487500 0.512500 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.492500 0.507500 (D) 0.491875 0.508125 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.377812 0.486250 0.513750 (D) Marker : SNP2 1 2 Alleles 0.523125 0.476875 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.523223 0.476777 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.309375 0.441250 0.558750 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.634750 0.365250 (D) 0.475000 0.525000 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.321523 0.588500 0.411500 (D) Marker : SNP3 1 2 Alleles 0.361875 0.638125 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.361875 0.638125 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.217188 0.262500 0.737500 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.495625 0.504375 (D) 0.271250 0.728750 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.227813 0.483750 0.516250 (D) Marker : STR1 1 2 3 Alleles 0.325625 0.335000 0.339375 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.325625 0.335000 0.339375 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.424063 0.300000 0.357500 0.342500 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.360000 0.305000 0.335000 (D) 0.306875 0.351875 0.341250 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.430312 0.351250 0.312500 0.336250 (D) Marker : STR2 1 2 3 Alleles 0.321875 0.331875 0.346250 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.321875 0.331875 0.346250 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.272188 0.315625 0.338750 0.345625 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.329375 0.322500 0.348125 (D) 0.330625 0.312500 0.356875 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.271875 0.308750 0.358125 0.333125 (D) Marker : STR3 1 2 3 Alleles 0.192875 0.212500 0.594625 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.192875 0.212500 0.594625 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.237500 0.074125 0.259375 0.666500 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.352875 0.150000 0.497125 (D) 0.060375 0.235625 0.704000 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.230313 0.371000 0.181875 0.447125 (D) Model-based (Phenotype: DISEASE_LOCUS) Marker : SNP1 1 2 Alleles 0.489375 0.510625 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.489375 0.510625 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.350937 0.506250 0.493750 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.386250 0.613750 (D) 0.506744 0.493256 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.359374 0.384813 0.615187 (D) Marker : SNP2 1 2 Alleles 0.523125 0.476875 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.523223 0.476777 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.106719 0.518173 0.481827 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.594972 0.405028 (D) 0.519477 0.480523 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.106953 0.602506 0.397494 (D) Marker : SNP3 1 2 Alleles 0.361875 0.638125 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.361875 0.638125 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.090313 0.307263 0.692737 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.691010 0.308990 (D) 0.305775 0.694225 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.098750 0.701394 0.298606 (D) Marker : STR1 1 2 3 Alleles 0.325625 0.335000 0.339375 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.325625 0.335000 0.339375 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.385937 0.331250 0.323125 0.345625 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.289375 0.408750 0.301875 (D) 0.325625 0.326875 0.347500 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.387501 0.325625 0.385000 0.289375 (D) Marker : STR2 1 2 3 Alleles 0.321875 0.331875 0.346250 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.321875 0.331875 0.346250 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.127500 0.316875 0.336250 0.346875 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.350000 0.304375 0.345625 (D) 0.330000 0.316875 0.353125 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.126249 0.269375 0.421250 0.309375 (D) Marker : STR3 1 2 3 Alleles 0.192875 0.212500 0.594625 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.192875 0.212500 0.594625 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.108750 0.101519 0.233750 0.664731 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.737875 0.086914 0.175211 (D) 0.094203 0.224375 0.681422 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.125000 0.772250 0.146250 0.081500 (D) Detail maximization info ======================== Dominant (Phenotype: DISEASE_LOCUS) Marker SNP1 Under H0: 5107.735617 7 14 0.500000 0.489375 0.510625 5107.735617 6 12 0.500000 0.489375 0.510625 Under H1: STEP 1 5107.969539 8 24 0.388750 0.500000 0.500000 5107.969539 5 18 0.388750 0.500000 0.500000 STEP 2 5107.543975 7 14 0.388750 0.489375 0.510625 5107.543975 6 12 0.388750 0.489375 0.510625 STEP 3 5107.543972 11 51 0.388437 0.489375 0.510625 5107.543972 6 31 0.388437 0.489375 0.510625 Under H2: STEP 1 5107.616524 10 39 0.500000 0.497500 0.502500 0.455000 0.545000 5107.613664 7 27 0.500000 0.496875 0.503125 0.458750 0.541250 5107.613664 6 23 0.500000 0.496875 0.503125 0.458750 0.541250 STEP 2 5107.614110 13 51 0.500000 0.495625 0.504375 0.461250 0.538750 5107.613628 6 23 0.500000 0.496250 0.503750 0.461250 0.538750 5107.613298 7 27 0.500000 0.496250 0.503750 0.460000 0.540000 5107.613298 6 23 0.500000 0.496250 0.503750 0.460000 0.540000 STEP 3 5107.614110 13 51 0.500000 0.495625 0.504375 0.461250 0.538750 5107.613628 6 23 0.500000 0.496250 0.503750 0.461250 0.538750 5107.613298 7 27 0.500000 0.496250 0.503750 0.460000 0.540000 5107.613298 6 23 0.500000 0.496250 0.503750 0.460000 0.540000 Under H3: STEP 1 5107.468445 11 72 0.395937 0.494375 0.505625 0.466875 0.533125 5107.468118 6 42 0.395937 0.494375 0.505625 0.468125 0.531875 5107.468107 7 48 0.395624 0.494375 0.505625 0.468125 0.531875 5107.468107 6 42 0.395624 0.494375 0.505625 0.468125 0.531875 STEP 2 5167.319987 8 31 0.050000 0.488125 0.511875 0.495625 0.504375 5167.319828 6 23 0.050000 0.488125 0.511875 0.496250 0.503750 5167.319828 6 23 0.050000 0.488125 0.511875 0.496250 0.503750 STEP 3 5107.471138 8 54 0.388750 0.493750 0.506250 0.470000 0.530000 5107.468178 8 54 0.394375 0.494375 0.505625 0.468125 0.531875 5107.468107 6 42 0.395625 0.494375 0.505625 0.468125 0.531875 5107.468107 6 42 0.395625 0.494375 0.505625 0.468125 0.531875 STEP 4 5107.477948 5 18 0.399375 0.496250 0.503750 0.460000 0.540000 5107.477948 5 18 0.399375 0.496250 0.503750 0.460000 0.540000 STEP 5 5107.469094 7 27 0.399375 0.494375 0.505625 0.466875 0.533125 5107.468922 6 23 0.399375 0.494375 0.505625 0.467500 0.532500 5107.468922 6 23 0.399375 0.494375 0.505625 0.467500 0.532500 STEP 6 5107.468107 9 60 0.395625 0.494375 0.505625 0.468125 0.531875 5107.468107 6 42 0.395625 0.494375 0.505625 0.468125 0.531875 STEP 7 5107.468626 13 84 0.393750 0.494375 0.505625 0.469375 0.530625 5107.468107 8 54 0.395625 0.494375 0.505625 0.468125 0.531875 5107.468107 6 42 0.395625 0.494375 0.505625 0.468125 0.531875 Marker SNP2 Under H0: 5131.054445 9 66 0.500000 0.523125 0.476875 5131.054445 8 58 0.500000 0.523125 0.476875 Under H1: STEP 1 5301.903897 6 20 0.143750 0.304000 0.696000 5301.903897 5 18 0.143750 0.304000 0.696000 STEP 2 5106.569192 9 66 0.143750 0.523125 0.476875 5106.569192 8 58 0.143750 0.523125 0.476875 STEP 3 5106.569446 11 111 0.144375 0.523125 0.476875 5106.569114 9 91 0.143828 0.523643 0.476357 5106.569115 8 81 0.143828 0.523643 0.476357 Under H2: STEP 1 5130.817644 19 183 0.500000 0.510000 0.490000 0.578500 0.421500 5130.816854 10 93 0.500000 0.510156 0.489844 0.579883 0.420117 5130.816853 9 83 0.500000 0.510156 0.489844 0.579883 0.420117 STEP 2 5131.053136 9 83 0.500000 0.523848 0.476152 0.524160 0.475840 5131.053140 8 73 0.500000 0.523848 0.476152 0.524160 0.475840 5131.053140 8 73 0.500000 0.523848 0.476152 0.524160 0.475840 STEP 3 5131.054366 8 73 0.500000 0.523643 0.476357 0.523643 0.476357 5131.054366 8 73 0.500000 0.523643 0.476357 0.523643 0.476357 Under H3: STEP 1 5105.040618 14 168 0.145078 0.506250 0.493750 0.593500 0.406500 5105.040617 9 108 0.145117 0.506250 0.493750 0.593500 0.406500 5105.040617 9 108 0.145117 0.506250 0.493750 0.593500 0.406500 STEP 2 5117.342900 9 83 0.050000 0.525121 0.474879 0.525746 0.474254 5117.342904 8 73 0.050000 0.525121 0.474879 0.525746 0.474254 5117.342904 8 73 0.050000 0.525121 0.474879 0.525746 0.474254 STEP 3 5106.559544 8 96 0.143828 0.525121 0.474879 0.525746 0.474254 5106.559544 8 96 0.143828 0.525121 0.474879 0.525746 0.474254 STEP 4 5105.095534 5 18 0.144453 0.510156 0.489844 0.579883 0.420117 5105.095534 5 18 0.144453 0.510156 0.489844 0.579883 0.420117 STEP 5 5105.077277 10 93 0.144453 0.510870 0.489130 0.586203 0.413797 5105.077275 9 83 0.144453 0.510870 0.489130 0.586203 0.413797 5105.077275 9 83 0.144453 0.510870 0.489130 0.586203 0.413797 STEP 6 5105.077273 10 120 0.144531 0.510870 0.489130 0.586203 0.413797 5105.077273 9 108 0.144531 0.510870 0.489130 0.586203 0.413797 STEP 7 5105.563317 15 180 0.143516 0.520314 0.479686 0.559849 0.440151 5105.563174 9 108 0.143516 0.520155 0.479845 0.559303 0.440697 5105.563165 9 108 0.143516 0.520155 0.479845 0.559303 0.440697 5105.563165 9 108 0.143516 0.520155 0.479845 0.559303 0.440697 Marker SNP3 Under H0: 5067.184932 11 22 0.500000 0.361875 0.638125 5067.184932 6 12 0.500000 0.361875 0.638125 Under H1: STEP 1 5113.614670 7 22 0.138750 0.500000 0.500000 5113.614670 5 18 0.138750 0.500000 0.500000 STEP 2 5040.753651 11 22 0.138750 0.361875 0.638125 5040.753651 6 12 0.138750 0.361875 0.638125 STEP 3 5040.753634 11 51 0.139063 0.361875 0.638125 5040.753634 6 31 0.139063 0.361875 0.638125 Under H2: STEP 1 5059.653294 22 87 0.500000 0.297500 0.702500 0.630000 0.370000 5059.646165 7 27 0.500000 0.296875 0.703125 0.636250 0.363750 5059.646165 6 23 0.500000 0.296875 0.703125 0.636250 0.363750 STEP 2 5059.649662 24 95 0.500000 0.297500 0.702500 0.631875 0.368125 5059.647674 6 23 0.500000 0.297500 0.702500 0.634375 0.365625 5059.647674 6 23 0.500000 0.297500 0.702500 0.634375 0.365625 STEP 3 5059.647427 20 79 0.500000 0.296865 0.703135 0.633798 0.366202 5059.646156 6 23 0.500000 0.296865 0.703135 0.636298 0.363702 5059.646156 6 23 0.500000 0.296865 0.703135 0.636298 0.363702 Under H3: STEP 1 5005.436787 15 96 0.142188 0.291875 0.708125 0.656250 0.343750 5005.434271 7 48 0.140625 0.291875 0.708125 0.656250 0.343750 5005.434271 6 42 0.140625 0.291875 0.708125 0.656250 0.343750 STEP 2 5018.593950 15 59 0.050000 0.300000 0.700000 0.622500 0.377500 5018.593950 6 23 0.050000 0.300000 0.700000 0.622500 0.377500 STEP 3 5005.435040 10 66 0.140313 0.292500 0.707500 0.655000 0.345000 5005.434986 6 42 0.140313 0.292500 0.707500 0.655625 0.344375 5005.434986 6 42 0.140313 0.292500 0.707500 0.655625 0.344375 STEP 4 5005.612854 6 20 0.137813 0.296865 0.703135 0.636298 0.363702 5005.612854 5 18 0.137813 0.296865 0.703135 0.636298 0.363702 STEP 5 5005.441421 10 39 0.137813 0.292490 0.707510 0.655048 0.344952 5005.441421 6 23 0.137813 0.292490 0.707510 0.655048 0.344952 STEP 6 5005.434635 7 48 0.140625 0.291865 0.708135 0.655048 0.344952 5005.434278 6 42 0.140625 0.291865 0.708135 0.655673 0.344327 5005.434278 6 42 0.140625 0.291865 0.708135 0.655673 0.344327 STEP 7 5005.441714 17 108 0.140313 0.291225 0.708775 0.659808 0.340192 5005.434399 8 54 0.140313 0.291850 0.708150 0.655433 0.344567 5005.434312 6 42 0.140313 0.291850 0.708150 0.656058 0.343942 5005.434252 6 42 0.140625 0.291850 0.708150 0.656058 0.343942 5005.434252 6 42 0.140625 0.291850 0.708150 0.656058 0.343942 Marker STR1 Under H0: 6080.870598 8 31 0.500000 0.325000 0.335000 0.340000 6080.868678 6 23 0.500000 0.325625 0.335000 0.339375 6080.868678 6 23 0.500000 0.325625 0.335000 0.339375 Under H1: STEP 1 6080.643323 8 24 0.398750 0.330000 0.330000 0.340000 6080.643323 5 18 0.398750 0.330000 0.330000 0.340000 STEP 2 6080.513153 8 31 0.398750 0.325000 0.335000 0.340000 6080.511233 6 23 0.398750 0.325625 0.335000 0.339375 6080.511233 6 23 0.398750 0.325625 0.335000 0.339375 STEP 3 6080.513389 11 72 0.400000 0.325000 0.335000 0.340000 6080.513153 7 48 0.398750 0.325000 0.335000 0.340000 6080.511233 6 42 0.398750 0.325625 0.335000 0.339375 6080.511233 6 42 0.398750 0.325625 0.335000 0.339375 Under H2: STEP 1 6080.058022 31 245 0.500000 0.345000 0.316250 0.338750 0.242500 0.415625 0.341875 6080.058022 6 45 0.500000 0.345000 0.316250 0.338750 0.242500 0.415625 0.341875 STEP 2 6080.058675 16 125 0.500000 0.345625 0.315000 0.339375 0.241250 0.419375 0.339375 6080.058552 7 53 0.500000 0.345625 0.315000 0.339375 0.241250 0.418750 0.340000 6080.058552 6 45 0.500000 0.345625 0.315000 0.339375 0.241250 0.418750 0.340000 Under H3: STEP 1 6079.909501 16 164 0.401250 0.334375 0.321250 0.344375 0.286250 0.395625 0.318125 6079.878556 12 124 0.407500 0.336875 0.318750 0.344375 0.278750 0.400625 0.320625 6079.864506 11 114 0.411250 0.336875 0.318125 0.345000 0.274375 0.408125 0.317500 6079.862446 6 64 0.411562 0.337500 0.318125 0.344375 0.274375 0.408125 0.317500 6079.859582 13 134 0.413749 0.338125 0.318125 0.343750 0.270625 0.410625 0.318750 6079.857380 7 74 0.413749 0.338125 0.317500 0.344375 0.270625 0.410625 0.318750 6079.857267 6 64 0.413749 0.338750 0.317500 0.343750 0.270625 0.410625 0.318750 6079.856339 8 84 0.414062 0.338750 0.317500 0.343750 0.269375 0.411250 0.319375 6079.855684 7 74 0.415312 0.338750 0.316875 0.344375 0.268750 0.411250 0.320000 6079.854848 7 74 0.414687 0.338750 0.316875 0.344375 0.268750 0.412500 0.318750 6079.854799 6 64 0.414687 0.338750 0.316875 0.344375 0.268750 0.413125 0.318125 6079.854799 6 64 0.414687 0.338750 0.316875 0.344375 0.268750 0.413125 0.318125 STEP 2 6208.812771 7 53 0.050000 0.325625 0.328750 0.345625 0.324375 0.362500 0.313125 6208.812485 7 53 0.050000 0.325625 0.328750 0.345625 0.323750 0.362500 0.313750 6208.812485 6 45 0.050000 0.325625 0.328750 0.345625 0.323750 0.362500 0.313750 STEP 3 6079.872502 18 184 0.409062 0.336250 0.318750 0.345000 0.278750 0.406250 0.315000 6079.867530 8 84 0.410000 0.336875 0.318750 0.344375 0.276250 0.406250 0.317500 6079.864289 9 94 0.411250 0.336875 0.318125 0.345000 0.274375 0.408750 0.316875 6079.862519 6 64 0.411562 0.337500 0.318125 0.344375 0.274375 0.408750 0.316875 6079.859741 8 84 0.411562 0.338125 0.318125 0.343750 0.270625 0.409375 0.320000 6079.859218 6 64 0.413749 0.338125 0.318125 0.343750 0.270625 0.409375 0.320000 6079.859218 6 64 0.413749 0.338125 0.318125 0.343750 0.270625 0.409375 0.320000 STEP 4 6079.922304 6 20 0.431875 0.345000 0.316250 0.338750 0.242500 0.415625 0.341875 6079.922304 5 18 0.431875 0.345000 0.316250 0.338750 0.242500 0.415625 0.341875 STEP 5 6079.872074 7 53 0.431875 0.341875 0.315625 0.342500 0.257500 0.415625 0.326875 6079.870219 6 45 0.431875 0.341875 0.315625 0.342500 0.257500 0.418125 0.324375 6079.870219 6 45 0.431875 0.341875 0.315625 0.342500 0.257500 0.418125 0.324375 STEP 6 6079.854023 7 74 0.419687 0.340625 0.315625 0.343750 0.262500 0.417500 0.320000 6079.853790 7 74 0.418125 0.340625 0.315625 0.343750 0.262500 0.417500 0.320000 6079.853790 6 64 0.418125 0.340625 0.315625 0.343750 0.262500 0.417500 0.320000 Marker STR2 Under H0: 6074.683524 9 35 0.500000 0.321875 0.331250 0.346875 6074.683109 6 23 0.500000 0.321875 0.331875 0.346250 6074.683109 6 23 0.500000 0.321875 0.331875 0.346250 Under H1: STEP 1 6043.002654 7 22 0.180625 0.330000 0.330000 0.340000 6043.002654 5 18 0.180625 0.330000 0.330000 0.340000 STEP 2 6042.648529 9 35 0.180625 0.321875 0.331250 0.346875 6042.648114 6 23 0.180625 0.321875 0.331875 0.346250 6042.648114 6 23 0.180625 0.321875 0.331875 0.346250 STEP 3 6042.648428 11 72 0.180938 0.321875 0.331250 0.346875 6042.648013 6 42 0.180938 0.321875 0.331875 0.346250 6042.648013 6 42 0.180938 0.321875 0.331875 0.346250 Under H2: STEP 1 6074.322808 15 117 0.500000 0.313125 0.326875 0.360000 0.355000 0.352500 0.292500 6074.307375 9 69 0.500000 0.312500 0.325000 0.362500 0.357500 0.360000 0.282500 6074.305132 6 45 0.500000 0.312500 0.325000 0.362500 0.360000 0.360625 0.279375 6074.305132 6 45 0.500000 0.312500 0.325000 0.362500 0.360000 0.360625 0.279375 STEP 2 6074.311324 20 157 0.500000 0.312500 0.326250 0.361250 0.356875 0.356875 0.286250 6074.308628 6 45 0.500000 0.312500 0.326250 0.361250 0.360000 0.356875 0.283125 6074.308628 6 45 0.500000 0.312500 0.326250 0.361250 0.360000 0.356875 0.283125 Under H3: STEP 1 6040.338301 18 184 0.179688 0.326250 0.313750 0.360000 0.297500 0.410000 0.292500 6040.337669 6 64 0.179688 0.326875 0.313750 0.359375 0.298125 0.410000 0.291875 6040.337669 6 64 0.179688 0.326875 0.313750 0.359375 0.298125 0.410000 0.291875 STEP 2 6079.019683 17 133 0.050000 0.326250 0.314375 0.359375 0.303125 0.401250 0.295625 6079.016915 6 45 0.050000 0.326250 0.315000 0.358750 0.303125 0.401250 0.295625 6079.016915 6 45 0.050000 0.326250 0.315000 0.358750 0.303125 0.401250 0.295625 STEP 3 6040.338233 10 104 0.180001 0.326250 0.313750 0.360000 0.298125 0.410625 0.291250 6040.338124 6 64 0.180001 0.326875 0.313750 0.359375 0.298125 0.410625 0.291250 6040.337215 7 74 0.180001 0.326875 0.313125 0.360000 0.298125 0.410000 0.291875 6040.337209 6 64 0.180001 0.326875 0.313125 0.360000 0.298125 0.410625 0.291250 6040.337209 6 64 0.180001 0.326875 0.313125 0.360000 0.298125 0.410625 0.291250 STEP 4 6041.857571 5 18 0.180626 0.312500 0.325000 0.362500 0.360000 0.360625 0.279375 6041.857571 5 18 0.180626 0.312500 0.325000 0.362500 0.360000 0.360625 0.279375 STEP 5 6040.339689 23 181 0.180626 0.327500 0.312500 0.360000 0.297500 0.410625 0.291875 6040.338759 6 45 0.180626 0.327500 0.313125 0.359375 0.297500 0.410625 0.291875 6040.338759 6 45 0.180626 0.327500 0.313125 0.359375 0.297500 0.410625 0.291875 STEP 6 6040.337289 8 84 0.180312 0.326875 0.313125 0.360000 0.297500 0.410625 0.291875 6040.337054 7 74 0.179687 0.326875 0.313125 0.360000 0.297500 0.410625 0.291875 6040.337054 6 64 0.179687 0.326875 0.313125 0.360000 0.297500 0.410625 0.291875 Marker STR3 Under H0: 5799.721580 9 35 0.500000 0.192875 0.212500 0.594625 5799.721580 6 23 0.500000 0.192875 0.212500 0.594625 Under H1: STEP 1 5822.999582 5 18 0.160000 0.106000 0.200000 0.694000 5822.999348 5 18 0.160625 0.106000 0.200000 0.694000 5822.999348 5 18 0.160625 0.106000 0.200000 0.694000 STEP 2 5754.831979 9 35 0.160625 0.192875 0.212500 0.594625 5754.831979 6 23 0.160625 0.192875 0.212500 0.594625 STEP 3 5754.831967 12 78 0.160312 0.192875 0.212500 0.594625 5754.831967 6 42 0.160312 0.192875 0.212500 0.594625 Under H2: STEP 1 5791.938884 44 349 0.500000 0.126000 0.215000 0.659000 0.471000 0.205000 0.324000 5791.927568 7 53 0.500000 0.125375 0.214375 0.660250 0.474750 0.207500 0.317750 5791.926368 6 45 0.500000 0.125375 0.214375 0.660250 0.476625 0.207500 0.315875 5791.926368 6 45 0.500000 0.125375 0.214375 0.660250 0.476625 0.207500 0.315875 STEP 2 5792.028362 33 261 0.500000 0.129125 0.214375 0.656500 0.455375 0.207500 0.337125 5791.926368 11 85 0.500000 0.125375 0.214375 0.660250 0.476625 0.207500 0.315875 5791.926368 6 45 0.500000 0.125375 0.214375 0.660250 0.476625 0.207500 0.315875 Under H3: STEP 1 5668.301500 21 214 0.162812 0.103516 0.213750 0.682734 0.571000 0.210000 0.219000 5668.294179 7 74 0.162812 0.103516 0.213750 0.682734 0.568500 0.208750 0.222750 5668.294101 6 64 0.163125 0.103516 0.213750 0.682734 0.568500 0.208750 0.222750 5668.294101 6 64 0.163125 0.103516 0.213750 0.682734 0.568500 0.208750 0.222750 STEP 2 5710.388658 15 117 0.050000 0.114750 0.215625 0.669625 0.512875 0.197500 0.289625 5710.348054 6 45 0.050000 0.114750 0.216250 0.669000 0.520375 0.198125 0.281500 5710.348054 6 45 0.050000 0.114750 0.216250 0.669000 0.520375 0.198125 0.281500 STEP 3 5668.308439 11 114 0.161562 0.104125 0.214375 0.681500 0.570375 0.208125 0.221500 5668.294667 7 74 0.162812 0.103500 0.213750 0.682750 0.569125 0.208125 0.222750 5668.294384 6 64 0.162812 0.103500 0.213750 0.682750 0.569125 0.208750 0.222125 5668.294245 6 64 0.163125 0.103500 0.213750 0.682750 0.569125 0.208750 0.222125 5668.294245 6 64 0.163125 0.103500 0.213750 0.682750 0.569125 0.208750 0.222125 STEP 4 5674.654799 5 18 0.154375 0.125375 0.214375 0.660250 0.476625 0.207500 0.315875 5674.654799 5 18 0.154375 0.125375 0.214375 0.660250 0.476625 0.207500 0.315875 STEP 5 5668.445999 14 109 0.154375 0.104125 0.213750 0.682125 0.566625 0.207500 0.225875 5668.445499 6 45 0.154375 0.104125 0.213750 0.682125 0.566625 0.208125 0.225250 5668.445499 6 45 0.154375 0.104125 0.213750 0.682125 0.566625 0.208125 0.225250 STEP 6 5668.297165 9 94 0.161875 0.103500 0.213750 0.682750 0.568500 0.208125 0.223375 5668.294157 6 64 0.162812 0.103500 0.213750 0.682750 0.568500 0.208750 0.222750 5668.294076 6 64 0.163125 0.103500 0.213750 0.682750 0.568500 0.208750 0.222750 5668.294076 6 64 0.163125 0.103500 0.213750 0.682750 0.568500 0.208750 0.222750 Recessive (Phenotype: DISEASE_LOCUS) Marker SNP1 Under H0: 9631.741431 7 14 0.500000 0.489375 0.510625 9631.741431 6 12 0.500000 0.489375 0.510625 Under H1: STEP 1 9631.139852 9 26 0.377500 0.500000 0.500000 9631.139852 5 18 0.377500 0.500000 0.500000 STEP 2 9630.714288 7 14 0.377500 0.489375 0.510625 9630.714288 6 12 0.377500 0.489375 0.510625 STEP 3 9630.714275 10 47 0.377812 0.489375 0.510625 9630.714275 6 31 0.377812 0.489375 0.510625 Under H2: STEP 1 9631.736559 7 27 0.500000 0.487500 0.512500 0.492500 0.507500 9631.736559 6 23 0.500000 0.487500 0.512500 0.492500 0.507500 STEP 2 9631.736559 8 31 0.500000 0.487500 0.512500 0.492500 0.507500 9631.736559 6 23 0.500000 0.487500 0.512500 0.492500 0.507500 STEP 3 9631.736559 8 31 0.500000 0.487500 0.512500 0.492500 0.507500 9631.736559 6 23 0.500000 0.487500 0.512500 0.492500 0.507500 Under H3: STEP 1 9630.706645 8 54 0.377812 0.492500 0.507500 0.485625 0.514375 9630.706645 6 42 0.377812 0.492500 0.507500 0.485625 0.514375 STEP 2 9803.641823 9 35 0.050000 0.481250 0.518750 0.499375 0.500625 9803.639898 6 23 0.050000 0.481250 0.518750 0.500625 0.499375 9803.639898 6 23 0.050000 0.481250 0.518750 0.500625 0.499375 STEP 3 9630.706144 13 84 0.377812 0.491875 0.508125 0.485625 0.514375 9630.705930 6 42 0.377812 0.491875 0.508125 0.486250 0.513750 9630.705930 6 42 0.377812 0.491875 0.508125 0.486250 0.513750 STEP 4 9630.737237 5 18 0.377812 0.487500 0.512500 0.492500 0.507500 9630.737237 5 18 0.377812 0.487500 0.512500 0.492500 0.507500 STEP 5 9630.706472 11 43 0.377812 0.491875 0.508125 0.486875 0.513125 9630.705930 7 27 0.377812 0.491875 0.508125 0.486250 0.513750 9630.705930 6 23 0.377812 0.491875 0.508125 0.486250 0.513750 STEP 6 9630.705930 10 66 0.377812 0.491875 0.508125 0.486250 0.513750 9630.705930 6 42 0.377812 0.491875 0.508125 0.486250 0.513750 STEP 7 9630.706177 10 66 0.377812 0.491250 0.508750 0.486875 0.513125 9630.706176 6 42 0.377812 0.491250 0.508750 0.486875 0.513125 Marker SNP2 Under H0: 9655.060259 9 66 0.500000 0.523125 0.476875 9655.060259 8 58 0.500000 0.523125 0.476875 Under H1: STEP 1 9844.822185 8 24 0.309375 0.304000 0.696000 9844.822185 5 18 0.309375 0.304000 0.696000 STEP 2 9649.487480 9 66 0.309375 0.523125 0.476875 9649.487480 8 58 0.309375 0.523125 0.476875 STEP 3 9649.487637 12 121 0.309375 0.523750 0.476250 9649.487311 8 81 0.309375 0.523223 0.476777 9649.487310 8 81 0.309375 0.523223 0.476777 Under H2: STEP 1 9650.147208 19 183 0.500000 0.441250 0.558750 0.634750 0.365250 9650.147208 10 93 0.500000 0.441250 0.558750 0.634750 0.365250 STEP 2 9655.037381 9 83 0.500000 0.525293 0.474707 0.526230 0.473770 9655.037401 8 73 0.500000 0.525293 0.474707 0.526230 0.473770 9655.037401 8 73 0.500000 0.525293 0.474707 0.526230 0.473770 STEP 3 9653.893420 9 83 0.500000 0.516507 0.483493 0.547516 0.452484 9653.893441 8 73 0.500000 0.516507 0.483493 0.547516 0.452484 9653.893441 8 73 0.500000 0.516507 0.483493 0.547516 0.452484 Under H3: STEP 1 9645.769157 15 180 0.321875 0.475000 0.525000 0.588500 0.411500 9645.769095 10 120 0.321523 0.475000 0.525000 0.588500 0.411500 9645.769095 9 108 0.321523 0.475000 0.525000 0.588500 0.411500 STEP 2 9796.256823 9 83 0.050000 0.526852 0.473148 0.528414 0.471586 9796.256871 8 73 0.050000 0.526852 0.473148 0.528414 0.471586 9796.256871 8 73 0.050000 0.526852 0.473148 0.528414 0.471586 STEP 3 9649.443577 8 96 0.309375 0.526013 0.473987 0.527214 0.472786 9649.443557 9 108 0.309297 0.526013 0.473987 0.527214 0.472786 9649.443557 8 96 0.309297 0.526013 0.473987 0.527214 0.472786 STEP 4 9647.151748 7 22 0.362500 0.441250 0.558750 0.634750 0.365250 9647.151748 5 18 0.362500 0.441250 0.558750 0.634750 0.365250 STEP 5 9646.481231 10 93 0.362500 0.454102 0.545898 0.603086 0.396914 9646.481216 9 83 0.362500 0.454102 0.545898 0.603086 0.396914 9646.481216 9 83 0.362500 0.454102 0.545898 0.603086 0.396914 STEP 6 9646.112137 25 300 0.328437 0.459122 0.540878 0.590717 0.409283 9646.111811 10 120 0.327578 0.459122 0.540878 0.590717 0.409283 9646.111811 9 108 0.327578 0.459122 0.540878 0.590717 0.409283 STEP 7 9647.839082 9 108 0.308672 0.517051 0.482949 0.549412 0.450588 9647.839093 8 96 0.308750 0.517051 0.482949 0.549412 0.450588 9647.839093 8 96 0.308750 0.517051 0.482949 0.549412 0.450588 Marker SNP3 Under H0: 9591.190746 11 22 0.500000 0.361875 0.638125 9591.190746 6 12 0.500000 0.361875 0.638125 Under H1: STEP 1 9640.565966 6 20 0.217500 0.500000 0.500000 9640.565966 5 18 0.217500 0.500000 0.500000 STEP 2 9567.704948 11 22 0.217500 0.361875 0.638125 9567.704948 6 12 0.217500 0.361875 0.638125 STEP 3 9567.704943 13 59 0.217188 0.361875 0.638125 9567.704943 6 31 0.217188 0.361875 0.638125 Under H2: STEP 1 9583.948380 14 55 0.500000 0.262500 0.737500 0.495000 0.505000 9583.947927 6 23 0.500000 0.262500 0.737500 0.495625 0.504375 9583.947927 6 23 0.500000 0.262500 0.737500 0.495625 0.504375 STEP 2 9583.948503 16 63 0.500000 0.261875 0.738125 0.496875 0.503125 9583.948112 7 27 0.500000 0.261875 0.738125 0.496250 0.503750 9583.948112 6 23 0.500000 0.261875 0.738125 0.496250 0.503750 STEP 3 9583.948190 15 59 0.500000 0.261870 0.738130 0.495962 0.504038 9583.947988 6 23 0.500000 0.262495 0.737505 0.495962 0.504038 9583.947988 6 23 0.500000 0.262495 0.737505 0.495962 0.504038 Under H3: STEP 1 9545.231790 20 126 0.228438 0.270625 0.729375 0.485000 0.515000 9545.231127 7 48 0.228126 0.270625 0.729375 0.484375 0.515625 9545.231127 6 42 0.228126 0.270625 0.729375 0.484375 0.515625 STEP 2 9632.337747 11 43 0.050000 0.298125 0.701875 0.448125 0.551875 9632.337747 6 23 0.050000 0.298125 0.701875 0.448125 0.551875 STEP 3 9545.232104 12 78 0.227500 0.271875 0.728125 0.483750 0.516250 9545.231053 7 48 0.227500 0.271250 0.728750 0.483750 0.516250 9545.230981 6 42 0.227813 0.271250 0.728750 0.483750 0.516250 9545.230981 6 42 0.227813 0.271250 0.728750 0.483750 0.516250 STEP 4 9545.422791 5 18 0.232188 0.262500 0.737500 0.495625 0.504375 9545.422791 5 18 0.232188 0.262500 0.737500 0.495625 0.504375 STEP 5 9545.249961 12 47 0.232188 0.270000 0.730000 0.485625 0.514375 9545.249961 6 23 0.232188 0.270000 0.730000 0.485625 0.514375 STEP 6 9545.232905 8 54 0.228437 0.270000 0.730000 0.485000 0.515000 9545.231789 6 42 0.228437 0.270625 0.729375 0.485000 0.515000 9545.231126 7 48 0.228125 0.270625 0.729375 0.484375 0.515625 9545.231126 6 42 0.228125 0.270625 0.729375 0.484375 0.515625 STEP 7 9545.231767 15 96 0.228125 0.270615 0.729385 0.485048 0.514952 9545.231148 7 48 0.228125 0.270615 0.729385 0.484423 0.515577 9545.231148 6 42 0.228125 0.270615 0.729385 0.484423 0.515577 Marker STR1 Under H0: 10604.876411 8 31 0.500000 0.325000 0.335000 0.340000 10604.874492 6 23 0.500000 0.325625 0.335000 0.339375 10604.874492 6 23 0.500000 0.325625 0.335000 0.339375 Under H1: STEP 1 10604.764176 5 18 0.423750 0.330000 0.330000 0.340000 10604.764176 5 18 0.423750 0.330000 0.330000 0.340000 STEP 2 10604.634007 8 31 0.423750 0.325000 0.335000 0.340000 10604.632087 6 23 0.423750 0.325625 0.335000 0.339375 10604.632087 6 23 0.423750 0.325625 0.335000 0.339375 STEP 3 10604.634159 8 54 0.425000 0.325000 0.335000 0.340000 10604.633998 7 48 0.424063 0.325000 0.335000 0.340000 10604.632079 6 42 0.424063 0.325625 0.335000 0.339375 10604.632079 6 42 0.424063 0.325625 0.335000 0.339375 Under H2: STEP 1 10604.406580 16 125 0.500000 0.300000 0.357500 0.342500 0.360000 0.305000 0.335000 10604.406580 6 45 0.500000 0.300000 0.357500 0.342500 0.360000 0.305000 0.335000 STEP 2 10604.413832 18 141 0.500000 0.302500 0.355000 0.342500 0.355625 0.308750 0.335625 10604.409999 7 53 0.500000 0.301875 0.355000 0.343125 0.358125 0.308125 0.333750 10604.409999 6 45 0.500000 0.301875 0.355000 0.343125 0.358125 0.308125 0.333750 Under H3: STEP 1 10604.293687 14 144 0.429063 0.306250 0.352500 0.341250 0.351250 0.312500 0.336250 10604.293378 6 64 0.430625 0.306250 0.352500 0.341250 0.351250 0.312500 0.336250 10604.293378 6 64 0.430625 0.306250 0.352500 0.341250 0.351250 0.312500 0.336250 STEP 2 10896.021986 10 77 0.050000 0.323125 0.336250 0.340625 0.329375 0.332500 0.338125 10896.021282 6 45 0.050000 0.323125 0.336875 0.340000 0.329375 0.332500 0.338125 10896.019885 7 53 0.050000 0.322500 0.336875 0.340625 0.329375 0.332500 0.338125 10896.019354 6 45 0.050000 0.322500 0.336875 0.340625 0.330000 0.332500 0.337500 10896.019354 6 45 0.050000 0.322500 0.336875 0.340625 0.330000 0.332500 0.337500 STEP 3 10604.294422 14 144 0.429688 0.307500 0.351875 0.340625 0.350625 0.312500 0.336875 10604.293249 7 74 0.430625 0.306875 0.351875 0.341250 0.350625 0.312500 0.336875 10604.293228 7 74 0.430312 0.306875 0.351875 0.341250 0.350625 0.312500 0.336875 10604.293138 6 64 0.430312 0.306875 0.351875 0.341250 0.351250 0.312500 0.336250 10604.293138 6 64 0.430312 0.306875 0.351875 0.341250 0.351250 0.312500 0.336250 STEP 4 10604.325740 5 18 0.437812 0.300000 0.357500 0.342500 0.360000 0.305000 0.335000 10604.325740 5 18 0.437812 0.300000 0.357500 0.342500 0.360000 0.305000 0.335000 STEP 5 10604.300016 12 93 0.437812 0.303750 0.353750 0.342500 0.354375 0.310000 0.335625 10604.299355 6 45 0.437812 0.304375 0.353750 0.341875 0.354375 0.310000 0.335625 10604.299355 6 45 0.437812 0.304375 0.353750 0.341875 0.354375 0.310000 0.335625 STEP 6 10604.295833 7 74 0.432812 0.304375 0.353750 0.341875 0.353750 0.310000 0.336250 10604.295812 7 74 0.432499 0.304375 0.353750 0.341875 0.353750 0.310000 0.336250 10604.295635 6 64 0.432499 0.305000 0.353750 0.341250 0.353750 0.310000 0.336250 10604.295183 7 74 0.432186 0.305000 0.353750 0.341250 0.353125 0.310000 0.336875 10604.294994 6 64 0.432186 0.305000 0.353750 0.341250 0.353125 0.310625 0.336250 10604.294994 6 64 0.432186 0.305000 0.353750 0.341250 0.353125 0.310625 0.336250 Marker STR2 Under H0: 10598.689337 9 35 0.500000 0.321875 0.331250 0.346875 10598.688922 6 23 0.500000 0.321875 0.331875 0.346250 10598.688922 6 23 0.500000 0.321875 0.331875 0.346250 Under H1: STEP 1 10582.877616 5 18 0.271875 0.330000 0.330000 0.340000 10582.877616 5 18 0.271875 0.330000 0.330000 0.340000 STEP 2 10582.523492 9 35 0.271875 0.321875 0.331250 0.346875 10582.523077 6 23 0.271875 0.321875 0.331875 0.346250 10582.523077 6 23 0.271875 0.321875 0.331875 0.346250 STEP 3 10582.523401 10 66 0.272188 0.321875 0.331250 0.346875 10582.522986 6 42 0.272188 0.321875 0.331875 0.346250 10582.522986 6 42 0.272188 0.321875 0.331875 0.346250 Under H2: STEP 1 10598.642154 11 85 0.500000 0.315625 0.340000 0.344375 0.329375 0.320000 0.350625 10598.640313 7 53 0.500000 0.315625 0.338750 0.345625 0.329375 0.322500 0.348125 10598.640313 6 45 0.500000 0.315625 0.338750 0.345625 0.329375 0.322500 0.348125 STEP 2 10598.642101 12 93 0.500000 0.316875 0.338750 0.344375 0.326875 0.322500 0.350625 10598.640313 7 53 0.500000 0.315625 0.338750 0.345625 0.329375 0.322500 0.348125 10598.640313 6 45 0.500000 0.315625 0.338750 0.345625 0.329375 0.322500 0.348125 Under H3: STEP 1 10581.551001 19 194 0.272188 0.330000 0.313125 0.356875 0.309375 0.357500 0.333125 10581.550809 7 74 0.271875 0.330000 0.313125 0.356875 0.309375 0.357500 0.333125 10581.550809 6 64 0.271875 0.330000 0.313125 0.356875 0.309375 0.357500 0.333125 STEP 2 10755.287069 15 117 0.050000 0.326875 0.319375 0.353750 0.313750 0.350000 0.336250 10755.287069 6 45 0.050000 0.326875 0.319375 0.353750 0.313750 0.350000 0.336250 STEP 3 10581.551795 14 144 0.271875 0.331250 0.311875 0.356875 0.308750 0.357500 0.333750 10581.550963 6 64 0.271875 0.331250 0.312500 0.356250 0.308750 0.358125 0.333125 10581.549848 7 74 0.271875 0.330625 0.312500 0.356875 0.308750 0.358125 0.333125 10581.549848 6 64 0.271875 0.330625 0.312500 0.356875 0.308750 0.358125 0.333125 STEP 4 10583.377748 5 18 0.273125 0.315625 0.338750 0.345625 0.329375 0.322500 0.348125 10583.377748 5 18 0.273125 0.315625 0.338750 0.345625 0.329375 0.322500 0.348125 STEP 5 10581.554255 15 117 0.273125 0.329375 0.313125 0.357500 0.309375 0.357500 0.333125 10581.552891 6 45 0.273125 0.330000 0.313125 0.356875 0.309375 0.357500 0.333125 10581.552891 6 45 0.273125 0.330000 0.313125 0.356875 0.309375 0.357500 0.333125 STEP 6 10581.550809 6 64 0.271875 0.330000 0.313125 0.356875 0.309375 0.357500 0.333125 10581.550809 6 64 0.271875 0.330000 0.313125 0.356875 0.309375 0.357500 0.333125 Marker STR3 Under H0: 10323.727393 9 35 0.500000 0.192875 0.212500 0.594625 10323.727393 6 23 0.500000 0.192875 0.212500 0.594625 Under H1: STEP 1 10366.148518 8 24 0.237500 0.106000 0.200000 0.694000 10366.148518 5 18 0.237500 0.106000 0.200000 0.694000 STEP 2 10297.981150 9 35 0.237500 0.192875 0.212500 0.594625 10297.981150 6 23 0.237500 0.192875 0.212500 0.594625 STEP 3 10297.981150 12 78 0.237500 0.192875 0.212500 0.594625 10297.981150 6 42 0.237500 0.192875 0.212500 0.594625 Under H2: STEP 1 10302.204504 22 173 0.500000 0.074750 0.258750 0.666500 0.351000 0.150000 0.499000 10302.202664 6 45 0.500000 0.074750 0.259375 0.665875 0.351625 0.150000 0.498375 10302.202664 6 45 0.500000 0.074750 0.259375 0.665875 0.351625 0.150000 0.498375 STEP 2 10302.201985 19 149 0.500000 0.074125 0.258750 0.667125 0.352875 0.150000 0.497125 10302.201479 6 45 0.500000 0.074125 0.259375 0.666500 0.352875 0.150000 0.497125 10302.201479 6 45 0.500000 0.074125 0.259375 0.666500 0.352875 0.150000 0.497125 Under H3: STEP 1 10210.066023 29 294 0.230000 0.061000 0.235625 0.703375 0.369750 0.182500 0.447750 10210.065134 7 74 0.230000 0.061000 0.235625 0.703375 0.369750 0.181875 0.448375 10210.064354 6 64 0.230000 0.061000 0.235625 0.703375 0.370375 0.181875 0.447750 10210.064354 6 64 0.230000 0.061000 0.235625 0.703375 0.370375 0.181875 0.447750 STEP 2 10348.751123 20 157 0.050000 0.082250 0.231250 0.686500 0.342875 0.186875 0.470250 10348.749318 6 45 0.050000 0.082250 0.231875 0.685875 0.342875 0.186875 0.470250 10348.745729 7 53 0.050000 0.081625 0.231875 0.686500 0.342250 0.186875 0.470875 10348.745596 6 45 0.050000 0.081625 0.232500 0.685875 0.342250 0.186875 0.470875 10348.745596 6 45 0.050000 0.081625 0.232500 0.685875 0.342250 0.186875 0.470875 STEP 3 10210.075733 19 194 0.231250 0.061000 0.235000 0.704000 0.372250 0.182500 0.445250 10210.065682 9 94 0.230000 0.061000 0.235000 0.704000 0.370375 0.181875 0.447750 10210.064354 6 64 0.230000 0.061000 0.235625 0.703375 0.370375 0.181875 0.447750 10210.064354 6 64 0.230000 0.061000 0.235625 0.703375 0.370375 0.181875 0.447750 STEP 4 10214.796927 6 20 0.229375 0.074125 0.259375 0.666500 0.352875 0.150000 0.497125 10214.796927 5 18 0.229375 0.074125 0.259375 0.666500 0.352875 0.150000 0.497125 STEP 5 10210.065565 17 133 0.229375 0.060375 0.236250 0.703375 0.370375 0.181875 0.447750 10210.065565 6 45 0.229375 0.060375 0.236250 0.703375 0.370375 0.181875 0.447750 STEP 6 10210.064034 8 84 0.230000 0.060375 0.235625 0.704000 0.370375 0.181875 0.447750 10210.063963 6 64 0.230313 0.060375 0.235625 0.704000 0.370375 0.181875 0.447750 10210.063930 6 64 0.230313 0.060375 0.235625 0.704000 0.371000 0.181875 0.447125 10210.063930 6 64 0.230313 0.060375 0.235625 0.704000 0.371000 0.181875 0.447125 Model-based (Phenotype: DISEASE_LOCUS) Marker SNP1 Under H0: 4275.067325 7 14 0.500000 0.489375 0.510625 4275.067325 6 12 0.500000 0.489375 0.510625 Under H1: STEP 1 4275.033581 6 20 0.351250 0.500000 0.500000 4275.033581 5 18 0.351250 0.500000 0.500000 STEP 2 4274.608017 7 14 0.351250 0.489375 0.510625 4274.608017 6 12 0.351250 0.489375 0.510625 STEP 3 4274.608037 9 43 0.351562 0.489375 0.510625 4274.608014 7 35 0.350937 0.489375 0.510625 4274.608014 6 31 0.350937 0.489375 0.510625 Under H2: STEP 1 4274.042271 11 43 0.500000 0.505625 0.494375 0.390000 0.610000 4274.041747 7 27 0.500000 0.505625 0.494375 0.388125 0.611875 4274.041294 6 23 0.500000 0.506250 0.493750 0.388125 0.611875 4274.040920 7 27 0.500000 0.506250 0.493750 0.386250 0.613750 4274.040920 6 23 0.500000 0.506250 0.493750 0.386250 0.613750 STEP 2 4274.043848 15 59 0.500000 0.505625 0.494375 0.391875 0.608125 4274.041747 7 27 0.500000 0.505625 0.494375 0.388125 0.611875 4274.041294 6 23 0.500000 0.506250 0.493750 0.388125 0.611875 4274.040920 7 27 0.500000 0.506250 0.493750 0.386250 0.613750 4274.040920 6 23 0.500000 0.506250 0.493750 0.386250 0.613750 STEP 3 4274.060163 8 31 0.500000 0.504244 0.495756 0.400438 0.599562 4274.042688 8 31 0.500000 0.505494 0.494506 0.390438 0.609562 4274.040969 8 31 0.500000 0.506119 0.493881 0.386688 0.613312 4274.040969 6 23 0.500000 0.506119 0.493881 0.386688 0.613312 Under H3: STEP 1 4273.266017 13 84 0.358749 0.506250 0.493750 0.385625 0.614375 4273.266017 6 42 0.358749 0.506250 0.493750 0.385625 0.614375 STEP 2 4303.432640 9 35 0.050000 0.499375 0.500625 0.429375 0.570625 4303.432640 6 23 0.050000 0.499375 0.500625 0.429375 0.570625 STEP 3 4273.266274 11 72 0.358437 0.506250 0.493750 0.386875 0.613125 4273.266034 7 48 0.358437 0.506250 0.493750 0.385625 0.614375 4273.266017 6 42 0.358749 0.506250 0.493750 0.385625 0.614375 4273.266017 6 42 0.358749 0.506250 0.493750 0.385625 0.614375 STEP 4 4273.266079 5 18 0.358749 0.506250 0.493750 0.386250 0.613750 4273.266079 5 18 0.358749 0.506250 0.493750 0.386250 0.613750 STEP 5 4273.266079 6 23 0.358749 0.506250 0.493750 0.386250 0.613750 4273.266079 6 23 0.358749 0.506250 0.493750 0.386250 0.613750 STEP 6 4273.266017 7 48 0.359063 0.506250 0.493750 0.385625 0.614375 4273.266017 6 42 0.359063 0.506250 0.493750 0.385625 0.614375 STEP 7 4273.294720 8 54 0.352812 0.504244 0.495756 0.400438 0.599562 4273.266131 14 90 0.358437 0.506744 0.493256 0.385438 0.614562 4273.265974 7 48 0.359062 0.506744 0.493256 0.384813 0.615187 4273.265974 6 42 0.359374 0.506744 0.493256 0.384813 0.615187 Marker SNP2 Under H0: 4298.386154 9 66 0.500000 0.523125 0.476875 4298.386154 8 58 0.500000 0.523125 0.476875 Under H1: STEP 1 4469.238530 5 18 0.106875 0.304000 0.696000 4469.238530 5 18 0.106875 0.304000 0.696000 STEP 2 4273.903826 9 66 0.106875 0.523125 0.476875 4273.903826 8 58 0.106875 0.523125 0.476875 STEP 3 4273.904122 9 91 0.106250 0.523750 0.476250 4273.903647 8 81 0.106719 0.523223 0.476777 4273.903646 8 81 0.106719 0.523223 0.476777 Under H2: STEP 1 4298.626435 10 93 0.500000 0.524500 0.475500 0.513250 0.486750 4298.626435 7 63 0.500000 0.524500 0.475500 0.513250 0.486750 STEP 2 4298.378761 9 83 0.500000 0.524570 0.475430 0.525195 0.474805 4298.378758 8 73 0.500000 0.524570 0.475430 0.525195 0.474805 4298.378758 8 73 0.500000 0.524570 0.475430 0.525195 0.474805 STEP 3 4297.136620 10 93 0.500000 0.518173 0.481827 0.594972 0.405028 4297.136608 9 83 0.500000 0.518173 0.481827 0.594972 0.405028 4297.136608 9 83 0.500000 0.518173 0.481827 0.594972 0.405028 Under H3: STEP 1 4274.477046 10 120 0.107149 0.524500 0.475500 0.513250 0.486750 4274.477046 7 84 0.107149 0.524500 0.475500 0.513250 0.486750 STEP 2 4276.515704 9 83 0.050000 0.526126 0.473874 0.527376 0.472624 4276.515707 8 73 0.050000 0.526126 0.473874 0.527376 0.472624 4276.515707 8 73 0.050000 0.526126 0.473874 0.527376 0.472624 STEP 3 4273.874005 8 96 0.106719 0.525718 0.474282 0.526792 0.473208 4273.874019 8 96 0.106719 0.525718 0.474282 0.526792 0.473208 4273.874019 8 96 0.106719 0.525718 0.474282 0.526792 0.473208 STEP 4 4271.275293 5 18 0.106719 0.518173 0.481827 0.594972 0.405028 4271.275293 5 18 0.106719 0.518173 0.481827 0.594972 0.405028 STEP 5 4271.250956 10 93 0.106719 0.519451 0.480549 0.602353 0.397647 4271.250969 9 83 0.106719 0.519451 0.480549 0.602353 0.397647 4271.250969 9 83 0.106719 0.519451 0.480549 0.602353 0.397647 STEP 6 4271.250938 9 108 0.106953 0.519451 0.480549 0.602353 0.397647 4271.250938 9 108 0.106953 0.519451 0.480549 0.602353 0.397647 STEP 7 4271.250942 11 132 0.106953 0.519477 0.480523 0.602506 0.397494 4271.250904 9 108 0.106953 0.519477 0.480523 0.602506 0.397494 4271.250904 9 108 0.106953 0.519477 0.480523 0.602506 0.397494 Marker SNP3 Under H0: 4234.516640 11 22 0.500000 0.361875 0.638125 4234.516640 6 12 0.500000 0.361875 0.638125 Under H1: STEP 1 4277.483038 6 20 0.090000 0.500000 0.500000 4277.483038 5 18 0.090000 0.500000 0.500000 STEP 2 4204.622020 11 22 0.090000 0.361875 0.638125 4204.622020 6 12 0.090000 0.361875 0.638125 STEP 3 4204.622020 17 75 0.090000 0.361875 0.638125 4204.621957 6 31 0.090313 0.361875 0.638125 4204.621957 6 31 0.090313 0.361875 0.638125 Under H2: STEP 1 4226.115382 19 75 0.500000 0.307500 0.692500 0.690000 0.310000 4226.115382 6 23 0.500000 0.307500 0.692500 0.690000 0.310000 STEP 2 4226.115478 27 107 0.500000 0.307500 0.692500 0.689375 0.310625 4226.115382 6 23 0.500000 0.307500 0.692500 0.690000 0.310000 4226.115382 6 23 0.500000 0.307500 0.692500 0.690000 0.310000 STEP 3 4226.115561 19 75 0.500000 0.307263 0.692737 0.689135 0.310865 4226.115130 6 23 0.500000 0.307263 0.692737 0.691010 0.308990 4226.115130 6 23 0.500000 0.307263 0.692737 0.691010 0.308990 Under H3: STEP 1 4169.961990 15 96 0.098437 0.306250 0.693750 0.700625 0.299375 4169.961922 6 42 0.098750 0.306250 0.693750 0.700625 0.299375 4169.961922 6 42 0.098750 0.306250 0.693750 0.700625 0.299375 STEP 2 4172.836148 18 71 0.050000 0.308750 0.691250 0.681875 0.318125 4172.836148 6 23 0.050000 0.308750 0.691250 0.681875 0.318125 STEP 3 4169.961922 11 72 0.098750 0.306250 0.693750 0.700625 0.299375 4169.961922 6 42 0.098750 0.306250 0.693750 0.700625 0.299375 STEP 4 4169.994139 6 20 0.097500 0.307263 0.692737 0.691010 0.308990 4169.994139 5 18 0.097500 0.307263 0.692737 0.691010 0.308990 STEP 5 4169.963013 7 27 0.097500 0.306013 0.693987 0.701010 0.298990 4169.962851 7 27 0.097500 0.306013 0.693987 0.700385 0.299615 4169.962851 6 23 0.097500 0.306013 0.693987 0.700385 0.299615 STEP 6 4169.961448 7 48 0.098750 0.306013 0.693987 0.700385 0.299615 4169.961446 6 42 0.098750 0.306013 0.693987 0.701010 0.298990 4169.961446 6 42 0.098750 0.306013 0.693987 0.701010 0.298990 STEP 7 4169.961372 13 84 0.098750 0.305775 0.694225 0.701394 0.298606 4169.961372 6 42 0.098750 0.305775 0.694225 0.701394 0.298606 Marker STR1 Under H0: 5248.202306 8 31 0.500000 0.325000 0.335000 0.340000 5248.200386 6 23 0.500000 0.325625 0.335000 0.339375 5248.200386 6 23 0.500000 0.325625 0.335000 0.339375 Under H1: STEP 1 5247.978681 8 24 0.385625 0.330000 0.330000 0.340000 5247.978681 5 18 0.385625 0.330000 0.330000 0.340000 STEP 2 5247.848511 8 31 0.385625 0.325000 0.335000 0.340000 5247.846591 6 23 0.385625 0.325625 0.335000 0.339375 5247.846591 6 23 0.385625 0.325625 0.335000 0.339375 STEP 3 5247.848757 11 72 0.387500 0.325000 0.335000 0.340000 5247.848501 7 48 0.385937 0.325000 0.335000 0.340000 5247.846582 6 42 0.385937 0.325625 0.335000 0.339375 5247.846582 6 42 0.385937 0.325625 0.335000 0.339375 Under H2: STEP 1 5247.716108 15 117 0.500000 0.330000 0.324375 0.345625 0.293750 0.402500 0.303750 5247.714166 6 45 0.500000 0.330625 0.324375 0.345000 0.293750 0.404375 0.301875 5247.711923 7 53 0.500000 0.330625 0.323750 0.345625 0.291250 0.404375 0.304375 5247.710243 6 45 0.500000 0.331250 0.323750 0.345000 0.291250 0.406250 0.302500 5247.709499 7 53 0.500000 0.331250 0.323750 0.345000 0.289375 0.406250 0.304375 5247.709443 6 45 0.500000 0.331250 0.323750 0.345000 0.289375 0.406875 0.303750 5247.709443 6 45 0.500000 0.331250 0.323750 0.345000 0.289375 0.406875 0.303750 STEP 2 5247.710785 18 141 0.500000 0.330625 0.323750 0.345625 0.290625 0.406875 0.302500 5247.709937 6 45 0.500000 0.331250 0.323750 0.345000 0.290625 0.406875 0.302500 5247.709068 7 53 0.500000 0.331250 0.323125 0.345625 0.289375 0.406875 0.303750 5247.708461 6 45 0.500000 0.331250 0.323125 0.345625 0.289375 0.408750 0.301875 5247.708461 6 45 0.500000 0.331250 0.323125 0.345625 0.289375 0.408750 0.301875 Under H3: STEP 1 5247.462091 9 94 0.380937 0.325000 0.328125 0.346875 0.330000 0.377500 0.292500 5247.456032 7 74 0.384687 0.325000 0.327500 0.347500 0.328125 0.382500 0.289375 5247.455727 6 64 0.386250 0.325000 0.327500 0.347500 0.328125 0.382500 0.289375 5247.455727 6 64 0.386250 0.325000 0.327500 0.347500 0.328125 0.382500 0.289375 STEP 2 5306.384435 9 69 0.050000 0.320000 0.334375 0.345625 0.356875 0.340000 0.303125 5306.384146 7 53 0.050000 0.320000 0.334375 0.345625 0.356875 0.339375 0.303750 5306.384141 6 45 0.050000 0.320000 0.334375 0.345625 0.357500 0.339375 0.303125 5306.384141 6 45 0.050000 0.320000 0.334375 0.345625 0.357500 0.339375 0.303125 STEP 3 5247.476092 18 184 0.380937 0.323125 0.329375 0.347500 0.337500 0.371250 0.291250 5247.455512 18 184 0.387187 0.325625 0.326875 0.347500 0.326250 0.383750 0.290000 5247.455394 6 64 0.387187 0.325625 0.326875 0.347500 0.326250 0.384375 0.289375 5247.455394 6 64 0.387187 0.325625 0.326875 0.347500 0.326250 0.384375 0.289375 STEP 4 5247.592702 7 22 0.408125 0.331250 0.323125 0.345625 0.289375 0.408750 0.301875 5247.592702 5 18 0.408125 0.331250 0.323125 0.345625 0.289375 0.408750 0.301875 STEP 5 5247.489634 17 133 0.408125 0.326250 0.326250 0.347500 0.320000 0.391250 0.288750 5247.489244 7 53 0.408125 0.326250 0.326250 0.347500 0.320000 0.390000 0.290000 5247.489244 6 45 0.408125 0.326250 0.326250 0.347500 0.320000 0.390000 0.290000 STEP 6 5247.457241 14 144 0.388125 0.326250 0.326250 0.347500 0.325000 0.386250 0.288750 5247.456936 7 74 0.388125 0.325625 0.326250 0.348125 0.324375 0.386250 0.289375 5247.456483 7 74 0.387813 0.325625 0.326250 0.348125 0.325625 0.386250 0.288125 5247.455839 6 64 0.387813 0.325625 0.326875 0.347500 0.325625 0.386250 0.288125 5247.455389 7 74 0.387501 0.325625 0.326875 0.347500 0.325625 0.385000 0.289375 5247.455389 6 64 0.387501 0.325625 0.326875 0.347500 0.325625 0.385000 0.289375 Marker STR2 Under H0: 5242.015232 9 35 0.500000 0.321875 0.331250 0.346875 5242.014817 6 23 0.500000 0.321875 0.331875 0.346250 5242.014817 6 23 0.500000 0.321875 0.331875 0.346250 Under H1: STEP 1 5206.794980 8 24 0.127500 0.330000 0.330000 0.340000 5206.794980 5 18 0.127500 0.330000 0.330000 0.340000 STEP 2 5206.440855 9 35 0.127500 0.321875 0.331250 0.346875 5206.440440 6 23 0.127500 0.321875 0.331875 0.346250 5206.440440 6 23 0.127500 0.321875 0.331875 0.346250 STEP 3 5206.440855 13 84 0.127500 0.321875 0.331250 0.346875 5206.440440 6 42 0.127500 0.321875 0.331875 0.346250 5206.440440 6 42 0.127500 0.321875 0.331875 0.346250 Under H2: STEP 1 5241.939781 13 101 0.500000 0.318125 0.334375 0.347500 0.335000 0.320000 0.345000 5241.914468 10 77 0.500000 0.318125 0.335000 0.346875 0.345000 0.311250 0.343750 5241.910334 9 69 0.500000 0.317500 0.335000 0.347500 0.347500 0.308750 0.343750 5241.909164 6 45 0.500000 0.317500 0.335625 0.346875 0.347500 0.308750 0.343750 5241.907599 8 61 0.500000 0.317500 0.336250 0.346250 0.348125 0.305000 0.346875 5241.905672 7 53 0.500000 0.316875 0.336250 0.346875 0.348125 0.305000 0.346875 5241.905082 7 53 0.500000 0.316875 0.336250 0.346875 0.349375 0.304375 0.346250 5241.904997 6 45 0.500000 0.316875 0.336250 0.346875 0.350000 0.304375 0.345625 5241.904997 6 45 0.500000 0.316875 0.336250 0.346875 0.350000 0.304375 0.345625 STEP 2 5241.904997 18 141 0.500000 0.316875 0.336250 0.346875 0.350000 0.304375 0.345625 5241.904997 6 45 0.500000 0.316875 0.336250 0.346875 0.350000 0.304375 0.345625 Under H3: STEP 1 5204.179679 12 124 0.126562 0.330000 0.316875 0.353125 0.270000 0.420000 0.310000 5204.179288 6 64 0.126562 0.330000 0.316875 0.353125 0.270000 0.421250 0.308750 5204.179044 7 74 0.126249 0.330000 0.316875 0.353125 0.269375 0.421250 0.309375 5204.179044 6 64 0.126249 0.330000 0.316875 0.353125 0.269375 0.421250 0.309375 STEP 2 5211.252331 14 109 0.050000 0.328750 0.317500 0.353750 0.274375 0.411875 0.313750 5211.245988 6 45 0.050000 0.329375 0.318125 0.352500 0.274375 0.414375 0.311250 5211.245988 6 45 0.050000 0.329375 0.318125 0.352500 0.274375 0.414375 0.311250 STEP 3 5204.180683 9 94 0.126875 0.329375 0.317500 0.353125 0.271250 0.419375 0.309375 5204.179938 9 94 0.126250 0.329375 0.317500 0.353125 0.270625 0.421250 0.308125 5204.179588 7 74 0.126250 0.329375 0.317500 0.353125 0.270000 0.420625 0.309375 5204.179588 6 64 0.126250 0.329375 0.317500 0.353125 0.270000 0.420625 0.309375 STEP 4 5208.238947 5 18 0.129375 0.316875 0.336250 0.346875 0.350000 0.304375 0.345625 5208.238947 5 18 0.129375 0.316875 0.336250 0.346875 0.350000 0.304375 0.345625 STEP 5 5204.190499 19 149 0.129375 0.330000 0.316250 0.353750 0.269375 0.421875 0.308750 5204.188186 6 45 0.129375 0.330000 0.316875 0.353125 0.269375 0.421875 0.308750 5204.188186 6 45 0.129375 0.330000 0.316875 0.353125 0.269375 0.421875 0.308750 STEP 6 5204.179139 9 94 0.126250 0.330000 0.316875 0.353125 0.269375 0.421875 0.308750 5204.179139 6 64 0.126250 0.330000 0.316875 0.353125 0.269375 0.421875 0.308750 Marker STR3 Under H0: 4967.053288 9 35 0.500000 0.192875 0.212500 0.594625 4967.053288 6 23 0.500000 0.192875 0.212500 0.594625 Under H1: STEP 1 4984.842543 5 18 0.108750 0.106000 0.200000 0.694000 4984.842543 5 18 0.108750 0.106000 0.200000 0.694000 STEP 2 4916.675175 9 35 0.108750 0.192875 0.212500 0.594625 4916.675175 6 23 0.108750 0.192875 0.212500 0.594625 STEP 3 4916.675626 13 84 0.108750 0.192250 0.212500 0.595250 4916.675175 6 42 0.108750 0.192875 0.212500 0.594625 4916.675175 6 42 0.108750 0.192875 0.212500 0.594625 Under H2: STEP 1 4927.288612 29 229 0.500000 0.101000 0.233750 0.665250 0.737250 0.087500 0.175250 4927.287762 7 53 0.500000 0.101000 0.233750 0.665250 0.738500 0.086875 0.174625 4927.287536 6 45 0.500000 0.101625 0.233750 0.664625 0.738500 0.086875 0.174625 4927.287279 7 53 0.500000 0.101625 0.233750 0.664625 0.737875 0.086875 0.175250 4927.287279 6 45 0.500000 0.101625 0.233750 0.664625 0.737875 0.086875 0.175250 STEP 2 4927.293826 30 237 0.500000 0.101519 0.232500 0.665981 0.736625 0.088164 0.175211 4927.287785 6 45 0.500000 0.101519 0.233750 0.664731 0.737875 0.088164 0.173961 4927.287014 7 53 0.500000 0.101519 0.233750 0.664731 0.737875 0.086914 0.175211 4927.287014 6 45 0.500000 0.101519 0.233750 0.664731 0.737875 0.086914 0.175211 Under H3: STEP 1 4775.574445 27 274 0.125000 0.093578 0.224375 0.682047 0.772250 0.146250 0.081500 4775.571587 6 64 0.125000 0.094203 0.224375 0.681422 0.772250 0.146250 0.081500 4775.571587 6 64 0.125000 0.094203 0.224375 0.681422 0.772250 0.146250 0.081500 STEP 2 4792.091288 24 189 0.050000 0.098766 0.223125 0.678109 0.737875 0.151875 0.110250 4792.089775 6 45 0.050000 0.099391 0.223125 0.677484 0.737875 0.151875 0.110250 4792.089775 6 45 0.050000 0.099391 0.223125 0.677484 0.737875 0.151875 0.110250 STEP 3 4775.578670 13 134 0.126250 0.094391 0.223125 0.682484 0.772875 0.146875 0.080250 4775.573309 8 84 0.125625 0.094391 0.223750 0.681859 0.771000 0.146875 0.082125 4775.572646 6 64 0.125625 0.094391 0.223750 0.681859 0.771625 0.146875 0.081500 4775.572065 7 74 0.125000 0.094391 0.223750 0.681859 0.771625 0.146875 0.081500 4775.572065 6 64 0.125000 0.094391 0.223750 0.681859 0.771625 0.146875 0.081500 STEP 4 4781.853200 6 20 0.122500 0.101519 0.233750 0.664731 0.737875 0.086914 0.175211 4781.853200 5 18 0.122500 0.101519 0.233750 0.664731 0.737875 0.086914 0.175211 STEP 5 4775.588211 13 101 0.122500 0.094644 0.223750 0.681606 0.772250 0.146914 0.080836 4775.587134 7 53 0.122500 0.094644 0.223750 0.681606 0.771625 0.146289 0.082086 4775.587134 6 45 0.122500 0.094644 0.223750 0.681606 0.771625 0.146289 0.082086 STEP 6 4775.572818 9 94 0.125000 0.094644 0.223750 0.681606 0.772250 0.146289 0.081461 4775.572818 6 64 0.125000 0.094644 0.223750 0.681606 0.772250 0.146289 0.081461 LD measures between disease and marker loci =========================================== Hypothesis H2: Linkage=No, LD=YES ================================= Dominant (Phenotype: DISEASE_LOCUS) Marker delta D' r r2 SNP1 -0.000004 -0.073041 0.000725 5.256021e-07 SNP2 0.000007 0.142333 0.001395 0.000002 SNP3 0.000034 0.482717 0.007429 0.000055 STR1 LD measures are only for SNP markers STR2 LD measures are only for SNP markers STR3 LD measures are only for SNP markers Recessive (Phenotype: DISEASE_LOCUS) Marker delta D' r r2 SNP1 4.999500e-07 0.009755 0.000100 1.000525e-08 SNP2 0.000019 0.346286 0.003897 0.000015 SNP3 0.000023 0.316080 0.005298 0.000028 STR1 LD measures are only for SNP markers STR2 LD measures are only for SNP markers STR3 LD measures are only for SNP markers Model-based (Phenotype: DISEASE_LOCUS) Marker delta D' r r2 SNP1 -0.001188 -0.235224 0.023881 0.000570 SNP2 0.000760 0.158049 0.015294 0.000234 SNP3 0.003799 0.551473 0.082477 0.006803 STR1 LD measures are only for SNP markers STR2 LD measures are only for SNP markers STR3 LD measures are only for SNP markers Hypothesis H3: Linkage=YES, LD=YES ================================== Dominant (Phenotype: DISEASE_LOCUS) Marker delta D' r r2 SNP1 -0.000003 -0.053092 0.000525 2.756324e-07 SNP2 0.000009 0.176694 0.001745 0.000003 SNP3 0.000036 0.514284 0.008011 0.000064 STR1 LD measures are only for SNP markers STR2 LD measures are only for SNP markers STR3 LD measures are only for SNP markers Recessive (Phenotype: DISEASE_LOCUS) Marker delta D' r r2 SNP1 -5.624438e-07 -0.011435 0.000113 1.265833e-08 SNP2 0.000011 0.216174 0.002273 0.000005 SNP3 0.000021 0.291575 0.004779 0.000023 STR1 LD measures are only for SNP markers STR2 LD measures are only for SNP markers STR3 LD measures are only for SNP markers Model-based (Phenotype: DISEASE_LOCUS) Marker delta D' r r2 SNP1 -0.001207 -0.238785 0.024265 0.000589 SNP2 0.000822 0.171357 0.016536 0.000273 SNP3 0.003917 0.567406 0.085132 0.007247 STR1 LD measures are only for SNP markers STR2 LD measures are only for SNP markers STR3 LD measures are only for SNP markers