------------------------------------------------------------------------------- Program PSEUDOMARKER 2.0 -- November (Andromeda Galaxy), 2013 (C) 2000-2013 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 http://www.helsinki.fi/~tsjuntun/pseudomarker ------------------------------------------------------------------------------- Date : Thu Nov 7 12:47:10 2013 Original articles: PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD. E. Michael Gertz, Tero Hiekkalinna, Sébastien Le Digabel, Charles Audet, Joseph D. Terwilliger and Alejandro A. Schäffer. Submitted. PSEUDOMARKER: A Powerful Program for Joint Linkage and/or Linkage Disequilibrium Analysis on Mixtures of Singletons and Related Individuals. T. Hiekkalinna, A. A. Schaffer, B. W. Lambert, P. Norrgrann, H.H.H. Göring, J.D. Terwilliger. Hum Hered 2011;71:256-266. 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. Göring and Joseph D. Terwilliger (Am. J. Hum. Genet. 66:1310-1327, 2000). 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 0.041815 SNP2 5.315007 SNP3 5.736650 STR1 0.077898 STR2 6.957008 STR3 9.744849 Recessive (Phenotype: DISEASE_LOCUS) Marker Linkage SNP1 0.223021 SNP2 1.210134 SNP3 5.099665 STR1 0.052646 STR2 3.510448 STR3 5.590519 Model-based (Phenotype: DISEASE_LOCUS) Marker Linkage SNP1 0.099738 SNP2 5.316272 SNP3 6.491548 STR1 0.076828 STR2 7.724878 STR3 10.939469 p-value statistics ================== Dominant (Phenotype: DISEASE_LOCUS) Marker Linkage LD|Linkage LD|NoLinkage Linkage|LD LD+Linkage SNP1 0.330406 0.782206 0.725924 0.702318 0.739098 SNP2 3.830131e-07 0.216362 0.625877 3.927651e-07 0.000001 SNP3 1.402413e-07 2.872779e-09 0.006046 1.889442e-13 2.164891e-14 STR1 0.274616 0.720977 0.667784 0.650382 0.700339 STR2 7.749958e-09 0.315814 0.827922 5.760735e-09 1.013250e-07 STR3 1.087072e-11 1.653481e-19 0.020323 1.126512e-28 1.520437e-28 Recessive (Phenotype: DISEASE_LOCUS) Marker Linkage LD|Linkage LD|NoLinkage Linkage|LD LD+Linkage SNP1 0.155419 0.926906 0.942865 0.310067 0.452368 SNP2 0.009131 0.053829 0.026678 0.036417 0.005957 SNP3 6.404814e-07 0.000002 0.007136 5.054324e-10 5.864541e-11 STR1 0.311235 0.843799 0.791372 0.735480 0.823995 STR2 0.000029 0.615402 0.976792 0.000036 0.000426 STR3 1.985990e-07 8.105577e-20 0.000021 8.628137e-22 9.974451e-25 Model-based (Phenotype: DISEASE_LOCUS) Marker Linkage LD|Linkage LD|NoLinkage Linkage|LD LD+Linkage SNP1 0.248981 0.246635 0.310987 0.378658 0.292895 SNP2 3.818591e-07 0.062798 0.116917 4.540964e-07 4.912234e-07 SNP3 2.334182e-08 4.033514e-09 0.003761 6.999866e-14 5.289930e-15 STR1 0.275994 0.822296 0.781723 0.615268 0.775756 STR2 1.262374e-09 0.323078 0.946893 8.392056e-10 1.837808e-08 STR3 6.595502e-13 2.289900e-31 2.317366e-09 0.000000e+00 5.880449e-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 0.192563 (1) 0.076422 (1) 0.122898 (1) 0.146087 (1) 0.268985 (50%:2 50%:1) SNP2 24.476514 (1) 1.528200 (1) 0.237725 (1) 25.766989 (1) 26.004714 (50%:2 50%:1) SNP3 26.418250 (1) 35.322432 (1) 7.541247 (1) 54.199435 (1) 61.740682 (50%:2 50%:1) STR1 0.358732 (1) 0.654296 (2) 0.807582 (2) 0.205446 (1) 1.013028 (50%:3 50%:2) STR2 32.038207 (1) 2.305206 (2) 0.377672 (2) 33.965741 (1) 34.343413 (50%:3 50%:2) STR3 44.876689 (1) 86.492468 (2) 7.791973 (2) 123.577184 (1) 131.369157 (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 1.027050 (1) 0.008411 (1) 0.005133 (1) 1.030328 (1) 1.035461 (50%:2 50%:1) SNP2 5.572874 (1) 3.718456 (1) 4.912939 (1) 4.378391 (1) 9.291330 (50%:2 50%:1) SNP3 23.484825 (1) 22.473746 (1) 7.242630 (1) 38.715941 (1) 45.958571 (50%:2 50%:1) STR1 0.242442 (1) 0.339681 (2) 0.467975 (2) 0.114148 (1) 0.582123 (50%:3 50%:2) STR2 16.166211 (1) 0.970959 (2) 0.046964 (2) 17.090206 (1) 17.137170 (50%:3 50%:2) STR3 25.745290 (1) 87.918299 (2) 21.527858 (2) 92.135731 (1) 113.663589 (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) 1.342152 (1) 1.026420 (1) 0.775044 (1) 1.801464 (50%:2 50%:1) SNP2 24.482338 (1) 3.462210 (1) 2.458050 (1) 25.486498 (1) 27.944548 (50%:2 50%:1) SNP3 29.894684 (1) 34.660563 (1) 8.401443 (1) 56.153804 (1) 64.555247 (50%:2 50%:1) STR1 0.353805 (1) 0.391311 (2) 0.492509 (2) 0.252607 (1) 0.745115 (50%:3 50%:2) STR2 35.574378 (1) 2.259725 (2) 0.109138 (2) 37.724966 (1) 37.834103 (50%:3 50%:2) STR3 50.378118 (1) 141.103260 (2) 39.765670 (2) 151.715708 (1) 191.481378 (50%:3 50%:2) -2ln(Likelihood) ================ Dominant (Phenotype: DISEASE_LOCUS) Marker H0 H1 H2 H3 SNP1 16989.066474 16988.873911 16988.943576 16988.797489 SNP2 17012.385009 16987.908495 17012.147284 16986.380295 SNP3 16948.515668 16922.097418 16940.974421 16886.774986 STR1 17962.199478 17961.840746 17961.391896 17961.186450 STR2 17956.012069 17923.973862 17955.634397 17921.668656 STR3 17681.051615 17636.174926 17673.259642 17549.682458 Recessive (Phenotype: DISEASE_LOCUS) Marker H0 H1 H2 H3 SNP1 22526.125747 22525.098697 22526.120614 22525.090286 SNP2 22549.444282 22543.871408 22544.531343 22540.152952 SNP3 22485.574941 22462.090116 22478.332311 22439.616370 STR1 23499.258751 23499.016309 23498.790776 23498.676628 STR2 23493.071342 23476.905131 23493.024378 23475.934172 STR3 23218.110887 23192.365597 23196.583029 23104.447298 Model-based (Phenotype: DISEASE_LOCUS) Marker H0 H1 H2 H3 SNP1 4275.067325 4274.608012 4274.040905 4273.265860 SNP2 4298.385860 4273.903522 4295.927810 4270.441312 SNP3 4234.516519 4204.621835 4226.115076 4169.961272 STR1 5248.200329 5247.846524 5247.707820 5247.455214 STR2 5242.012920 5206.438542 5241.903782 5204.178817 STR3 4967.052465 4916.674347 4927.286796 4775.571088 Maximized allele and haplotype frequencies ========================================== Dominant (Phenotype: DISEASE_LOCUS) Marker : SNP1 1 2 Alleles 0.489362 0.510638 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.489362 0.510638 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.388424 0.496380 0.503620 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.459736 0.540264 (D) 0.494456 0.505544 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.395479 0.467857 0.532143 (D) Marker : SNP2 1 2 Alleles 0.523404 0.476596 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.523404 0.476596 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.143830 0.509260 0.490740 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.583110 0.416890 (D) 0.506913 0.493087 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.145112 0.593019 0.406981 (D) Marker : SNP3 1 2 Alleles 0.361702 0.638298 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.361702 0.638298 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.139024 0.296544 0.703456 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.636748 0.363252 (D) 0.292016 0.707984 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.140586 0.655867 0.344133 (D) Marker : STR1 1 2 3 Alleles 0.325532 0.335106 0.339362 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.325532 0.335106 0.339362 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.398533 0.345416 0.315879 0.338705 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.241596 0.416270 0.342134 (D) 0.339821 0.316006 0.344173 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.416620 0.265213 0.415733 0.319053 (D) Marker : STR2 1 2 3 Alleles 0.321277 0.331915 0.346808 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.321277 0.331915 0.346808 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.180835 0.311541 0.325046 0.363413 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.362372 0.360909 0.276718 (D) 0.326875 0.313350 0.359775 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.179761 0.297578 0.410273 0.292148 (D) Marker : STR3 1 2 3 Alleles 0.192553 0.212766 0.594681 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.192553 0.212766 0.594681 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.160471 0.125048 0.213547 0.661406 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.477507 0.209470 0.313023 (D) 0.103465 0.213633 0.682902 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.163318 0.568535 0.209106 0.222358 (D) Recessive (Phenotype: DISEASE_LOCUS) Marker : SNP1 1 2 Alleles 0.489362 0.510638 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.489362 0.510638 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.377743 0.487221 0.512779 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.492252 0.507748 (D) 0.491666 0.508334 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.377820 0.486251 0.513749 (D) Marker : SNP2 1 2 Alleles 0.523404 0.476596 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.523404 0.476596 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.309341 0.440964 0.559036 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.634692 0.365308 (D) 0.475110 0.524890 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.321510 0.588597 0.411403 (D) Marker : SNP3 1 2 Alleles 0.361702 0.638298 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.361702 0.638298 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.217337 0.262353 0.737647 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.495815 0.504185 (D) 0.271032 0.728968 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.227870 0.484100 0.515900 (D) Marker : STR1 1 2 3 Alleles 0.325532 0.335106 0.339362 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.325532 0.335106 0.339362 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.423987 0.300117 0.357344 0.342539 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.359883 0.305098 0.335020 (D) 0.306215 0.351659 0.342126 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.430540 0.351609 0.312761 0.335630 (D) Marker : STR2 1 2 3 Alleles 0.321277 0.331915 0.346808 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.321277 0.331915 0.346808 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.272156 0.315474 0.339033 0.345493 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.329097 0.322310 0.348594 (D) 0.330549 0.312518 0.356933 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.271787 0.308760 0.358101 0.333140 (D) Marker : STR3 1 2 3 Alleles 0.192553 0.212766 0.594681 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.192553 0.212766 0.594681 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.237348 0.074084 0.259449 0.666468 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.352478 0.149748 0.497774 (D) 0.060593 0.235884 0.703523 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.230182 0.370690 0.181558 0.447752 (D) Model-based (Phenotype: DISEASE_LOCUS) Marker : SNP1 1 2 Alleles 0.489362 0.510638 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.489362 0.510638 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.351025 0.506297 0.493703 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.386404 0.613596 (D) 0.506525 0.493475 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.359118 0.385013 0.614987 (D) Marker : SNP2 1 2 Alleles 0.523404 0.476596 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.523404 0.476596 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.106746 0.492782 0.507218 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.708539 0.291461 (D) 0.503572 0.496428 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.110384 0.644155 0.355845 (D) Marker : SNP3 1 2 Alleles 0.361702 0.638298 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.361702 0.638298 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.090282 0.307125 0.692875 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.691080 0.308920 (D) 0.305806 0.694194 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.098781 0.700863 0.299137 (D) Marker : STR1 1 2 3 Alleles 0.325532 0.335106 0.339362 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.325532 0.335106 0.339362 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.385925 0.331819 0.322841 0.345340 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.287306 0.409681 0.303013 (D) 0.325349 0.327029 0.347622 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.387075 0.326642 0.384202 0.289156 (D) Marker : STR2 1 2 3 Alleles 0.321277 0.331915 0.346808 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.321277 0.331915 0.346808 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.127529 0.316142 0.336879 0.346980 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.352451 0.301781 0.345767 (D) 0.329842 0.317132 0.353027 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.126122 0.269651 0.421022 0.309326 (D) Marker : STR3 1 2 3 Alleles 0.192553 0.212766 0.594681 Allele frequencies under H0 (Linkage=No, LD=No) Thetas: 0.500000 0.192553 0.212766 0.594681 Allele frequencies under H1 (Linkage=YES,LD=No) Thetas: 0.108812 0.101356 0.233896 0.664748 (+) Conditional allele frequencies under H2 (Linkage=No, LD=YES) Thetas: 0.500000 0.738192 0.086343 0.175465 (D) 0.094202 0.224088 0.681711 (+) Conditional allele frequencies under H3 (Linkage=YES,LD=YES) Thetas: 0.125148 0.772469 0.146009 0.081522 (D) Detail maximization info ======================== Dominant (Phenotype: DISEASE_LOCUS) Marker SNP1 H0: 16989.066474 20 36 0.500000 0.489362 0.510638 H1: 16988.873911 32 104 0.388424 0.489362 0.510638 H2: 16988.943576 26 89 0.500000 0.496380 0.503620 0.459736 0.540264 H3: 16988.797489 38 174 0.395479 0.494456 0.505544 0.467857 0.532143 Marker SNP2 H0: 17012.385009 30 48 0.500000 0.523404 0.476596 H1: 16987.908495 38 111 0.143830 0.523404 0.476596 H2: 17012.147284 42 114 0.500000 0.509260 0.490740 0.583110 0.416890 H3: 16986.380295 42 181 0.145112 0.506913 0.493087 0.593019 0.406981 Marker SNP3 H0: 16948.515668 26 43 0.500000 0.361702 0.638298 H1: 16922.097418 36 111 0.139024 0.361702 0.638298 H2: 16940.974421 40 118 0.500000 0.296544 0.703456 0.636748 0.363252 H3: 16886.774986 38 169 0.140586 0.292016 0.707984 0.655867 0.344133 Marker STR1 H0: 17962.199478 22 74 0.500000 0.325532 0.335106 0.339362 H1: 17961.840746 40 174 0.398533 0.325532 0.335106 0.339362 H2: 17961.391896 50 309 0.500000 0.345416 0.315879 0.338705 0.241596 0.416270 0.342134 H3: 17961.186450 66 464 0.416620 0.339821 0.316006 0.344173 0.265213 0.415733 0.319053 Marker STR2 H0: 17956.012069 30 96 0.500000 0.321277 0.331915 0.346808 H1: 17923.973862 40 184 0.180835 0.321277 0.331915 0.346808 H2: 17955.634397 46 273 0.500000 0.311541 0.325046 0.363413 0.362372 0.360909 0.276718 H3: 17921.668656 36 268 0.179761 0.326875 0.313350 0.359775 0.297578 0.410273 0.292148 Marker STR3 H0: 17681.051615 30 98 0.500000 0.192553 0.212766 0.594681 H1: 17636.174926 48 216 0.160471 0.192553 0.212766 0.594681 H2: 17673.259642 60 384 0.500000 0.125048 0.213547 0.661406 0.477507 0.209470 0.313023 H3: 17549.682458 56 411 0.163318 0.103465 0.213633 0.682902 0.568535 0.209106 0.222358 Recessive (Phenotype: DISEASE_LOCUS) Marker SNP1 H0: 22526.125747 20 36 0.500000 0.489362 0.510638 H1: 22525.098697 40 119 0.377743 0.489362 0.510638 H2: 22526.120614 28 91 0.500000 0.487221 0.512779 0.492252 0.507748 H3: 22525.090286 32 154 0.377820 0.491666 0.508334 0.486251 0.513749 Marker SNP2 H0: 22549.444282 30 48 0.500000 0.523404 0.476596 H1: 22543.871408 42 111 0.309341 0.523404 0.476596 H2: 22544.531343 38 115 0.500000 0.440964 0.559036 0.634692 0.365308 H3: 22540.152952 52 235 0.321510 0.475110 0.524890 0.588597 0.411403 Marker SNP3 H0: 22485.574941 26 43 0.500000 0.361702 0.638298 H1: 22462.090116 42 134 0.217337 0.361702 0.638298 H2: 22478.332311 32 101 0.500000 0.262353 0.737647 0.495815 0.504185 H3: 22439.616370 38 170 0.227870 0.271032 0.728968 0.484100 0.515900 Marker STR1 H0: 23499.258751 22 74 0.500000 0.325532 0.335106 0.339362 H1: 23499.016309 54 227 0.423987 0.325532 0.335106 0.339362 H2: 23498.790776 20 140 0.500000 0.300117 0.357344 0.342539 0.359883 0.305098 0.335020 H3: 23498.676628 56 401 0.430540 0.306215 0.351659 0.342126 0.351609 0.312761 0.335630 Marker STR2 H0: 23493.071342 30 96 0.500000 0.321277 0.331915 0.346808 H1: 23476.905131 32 144 0.272156 0.321277 0.331915 0.346808 H2: 23493.024378 26 178 0.500000 0.315474 0.339033 0.345493 0.329097 0.322310 0.348594 H3: 23475.934172 42 293 0.271787 0.330549 0.312518 0.356933 0.308760 0.358101 0.333140 Marker STR3 H0: 23218.110887 30 98 0.500000 0.192553 0.212766 0.594681 H1: 23192.365597 46 211 0.237348 0.192553 0.212766 0.594681 H2: 23196.583029 52 311 0.500000 0.074084 0.259449 0.666468 0.352478 0.149748 0.497774 H3: 23104.447298 46 368 0.230182 0.060593 0.235884 0.703523 0.370690 0.181558 0.447752 Model-based (Phenotype: DISEASE_LOCUS) Marker SNP1 H0: 4275.067325 20 36 0.500000 0.489362 0.510638 H1: 4274.608012 30 94 0.351025 0.489362 0.510638 H2: 4274.040905 30 96 0.500000 0.506297 0.493703 0.386404 0.613596 H3: 4273.265860 36 173 0.359118 0.506525 0.493475 0.385013 0.614987 Marker SNP2 H0: 4298.385860 30 48 0.500000 0.523404 0.476596 H1: 4273.903522 36 115 0.106746 0.523404 0.476596 H2: 4295.927810 42 122 0.500000 0.492782 0.507218 0.708539 0.291461 H3: 4270.441312 40 179 0.110384 0.503572 0.496428 0.644155 0.355845 Marker SNP3 H0: 4234.516519 26 43 0.500000 0.361702 0.638298 H1: 4204.621835 38 120 0.090282 0.361702 0.638298 H2: 4226.115076 48 146 0.500000 0.307125 0.692875 0.691080 0.308920 H3: 4169.961272 38 178 0.098781 0.305806 0.694194 0.700863 0.299137 Marker STR1 H0: 5248.200329 22 74 0.500000 0.325532 0.335106 0.339362 H1: 5247.846524 46 194 0.385925 0.325532 0.335106 0.339362 H2: 5247.707820 42 259 0.500000 0.331819 0.322841 0.345340 0.287306 0.409681 0.303013 H3: 5247.455214 32 249 0.387075 0.325349 0.327029 0.347622 0.326642 0.384202 0.289156 Marker STR2 H0: 5242.012920 30 96 0.500000 0.321277 0.331915 0.346808 H1: 5206.438542 38 167 0.127529 0.321277 0.331915 0.346808 H2: 5241.903782 48 294 0.500000 0.316142 0.336879 0.346980 0.352451 0.301781 0.345767 H3: 5204.178817 44 326 0.126122 0.329842 0.317132 0.353027 0.269651 0.421022 0.309326 Marker STR3 H0: 4967.052465 30 98 0.500000 0.192553 0.212766 0.594681 H1: 4916.674347 48 216 0.108812 0.192553 0.212766 0.594681 H2: 4927.286796 66 402 0.500000 0.101356 0.233896 0.664748 0.738192 0.086343 0.175465 H3: 4775.571088 58 406 0.125148 0.094202 0.224088 0.681711 0.772469 0.146009 0.081522 LD measures between disease and marker loci =========================================== Hypothesis H2: Linkage=No, LD=YES ================================= Dominant (Phenotype: DISEASE_LOCUS) Marker delta D' r r2 SNP1 -3.664362e-07 -0.073822 0.000232 5.371354e-08 SNP2 7.384913e-07 0.150486 0.000467 2.182248e-07 SNP3 0.000003 0.483616 0.002355 0.000006 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 5.030772e-08 0.009811 0.000032 1.013019e-09 SNP2 0.000002 0.346538 0.001234 0.000002 SNP3 0.000002 0.316494 0.001678 0.000003 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 -0.001187 -0.234992 0.023860 0.000569 SNP2 0.002136 0.422919 0.042937 0.001844 SNP3 0.003801 0.551663 0.082532 0.006811 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 -2.659924e-07 -0.053795 0.000168 2.830454e-08 SNP2 8.610563e-07 0.174626 0.000545 2.966269e-07 SNP3 0.000004 0.513923 0.002530 0.000006 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 -5.415672e-08 -0.011015 0.000034 1.173518e-09 SNP2 0.000001 0.216210 0.000719 5.164487e-07 SNP3 0.000002 0.292285 0.001516 0.000002 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 -0.001203 -0.238066 0.024182 0.000585 SNP2 0.001392 0.281154 0.027977 0.000783 SNP3 0.003911 0.566621 0.085009 0.007227 STR1 LD measures are only for SNP markers STR2 LD measures are only for SNP markers STR3 LD measures are only for SNP markers