# hapMC Haplotype report ``` ********** hapMC - production version 2.0 Report ********** Created: Mon Oct 09 11:17:17 MDT 2006 Specification from: Haplotype.rgen Data from: ./GenotypeData.dat Runtime global parameters: ccstat1=ChiSquared ccstat2=ChiSquaredTrend ccstat3=OddsRatios ccstat4=Quantitative covar1=1 drop=HapMCDropSim locus 1=SNP1 locus 2=SNP2 nsims=2000 report=report rseed=777 top=HapMCTopSim top-sample=all ________________________________________________________________ *** Analysis 1 *** Loci : ALL MARKERS Model : Hap 2 vs Hap 1 Type : Genotype *** Study : Testing ================= Contingency Table ================= Pheno Type ---------------- Col(wt) ---------------- 1(0) 2(1) TOTAL Case : 0 32 32 Control : 32 16 48 -- TOTAL : 32 48 80 ================= Quantitative Table ================= CoVar Mean ---------------- Col(wt) ---------------- 1(0) 2(1) Row Total CoVar-0 : 2.055484 2.197273 4.252757 -- Col TOTAL : 2.055484 2.197273 4.252757 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 35.555556 Empirical p-value : 0.0005 Odds Ratios, 2-Tailed Test : 0 / 2000 total statistics calculated Observed statistic : WARNING: reference cell has 0 value, **test** has not been performed. Empirical p-value : - Empirical Confidence Intervals : (-, -) Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:0.833911 Empirical p-value : 2v1:0.4115 ________________________________________________________________ *** Analysis 2 *** Loci : ALL MARKERS Model : Hap 3 vs Hap 1 Type : Genotype *** Study : Testing ================= Contingency Table ================= Pheno Type ---------------- Col(wt) ---------------- 1(0) 2(1) TOTAL Case : 0 16 16 Control : 48 0 48 -- TOTAL : 48 16 64 ================= Quantitative Table ================= CoVar Mean ---------------- Col(wt) ---------------- 1(0) 2(1) Row Total CoVar-0 : 2.071087 1.975385 4.046472 -- Col TOTAL : 2.071087 1.975385 4.046472 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 64 Empirical p-value : 0 Odds Ratios, 2-Tailed Test : 0 / 2000 total statistics calculated Observed statistic : WARNING: reference cell has 0 value, **test** has not been performed. Empirical p-value : - Empirical Confidence Intervals : (-, -) Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:-0.498144 Empirical p-value : 2v1:0.615 ________________________________________________________________ *** Analysis 3 *** Loci : ALL MARKERS Model : Hap 4 vs Hap 1 Type : Genotype *** Study : Testing ================= Contingency Table ================= Pheno Type ---------------- Col(wt) ---------------- 1(0) 2(1) TOTAL Case : 0 32 32 Control : 16 48 64 -- TOTAL : 16 80 96 ================= Quantitative Table ================= CoVar Mean ---------------- Col(wt) ---------------- 1(0) 2(1) Row Total CoVar-0 : 2.103333 2.108219 4.211553 -- Col TOTAL : 2.103333 2.108219 4.211553 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 9.6 Empirical p-value : 0.002 Odds Ratios, 2-Tailed Test : 0 / 2000 total statistics calculated Observed statistic : WARNING: reference cell has 0 value, **test** has not been performed. Empirical p-value : - Empirical Confidence Intervals : (-, -) Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 2v1:0.024777 Empirical p-value : 2v1:0.9785 ________________________________________________________________ *** Analysis 4 *** Loci : ALL MARKERS Model : Hap 2 vs rest REV Type : Genotype *** Study : Testing ================= Contingency Table ================= Pheno Type ---------------- Col(wt) ---------------- 1(1) 2(0) TOTAL Case : 32 16 48 Control : 16 48 64 -- TOTAL : 48 64 112 ================= Quantitative Table ================= CoVar Mean ---------------- Col(wt) ---------------- 1(1) 2(0) Row Total CoVar-0 : 2.197273 2.085439 4.282711 -- Col TOTAL : 2.197273 2.085439 4.282711 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 19.444444 Empirical p-value : 0.001 Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 1v2:6 Empirical p-value : 1v2:0 Empirical Confidence Intervals : (2.726267, 13.204868) Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 1v2:0.749856 Empirical p-value : 1v2:0.4515 ________________________________________________________________ *** Analysis 5 *** Loci : ALL MARKERS Model : Hap 3 vs rest REV Type : Genotype *** Study : Testing ================= Contingency Table ================= Pheno Type ---------------- Col(wt) ---------------- 1(1) 2(0) TOTAL Case : 16 32 48 Control : 0 64 64 -- TOTAL : 16 96 112 ================= Quantitative Table ================= CoVar Mean ---------------- Col(wt) ---------------- 1(1) 2(0) Row Total CoVar-0 : 1.975385 2.157614 4.132998 -- Col TOTAL : 1.975385 2.157614 4.132998 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 24.888889 Empirical p-value : 0.001 Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 1v2:- Empirical p-value : 1v2:0.002 Empirical Confidence Intervals : (-, -) Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 1v2:-1.002694 Empirical p-value : 1v2:0.324 ________________________________________________________________ *** Analysis 6 *** Loci : ALL MARKERS Model : Hap 4 vs rest Type : Genotype *** Study : Testing ================= Contingency Table ================= Pheno Type ---------------- Col(wt) ---------------- 1(1) 2(0) TOTAL Case : 32 16 48 Control : 48 16 64 -- TOTAL : 80 32 112 ================= Quantitative Table ================= CoVar Mean ---------------- Col(wt) ---------------- 1(1) 2(0) Row Total CoVar-0 : 2.108219 2.201786 4.310005 -- Col TOTAL : 2.108219 2.201786 4.310005 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 0.933333 Empirical p-value : 0.35 Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 1v2:0.666667 Empirical p-value : 1v2:0.351 Empirical Confidence Intervals : (0.304403, 1.460055) Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 1v2:-0.57367 Empirical p-value : 1v2:0.567 ________________________________________________________________ *** Analysis 7 *** Loci : ALL MARKERS Model : Hap 3 Dom REV Type : Genotype *** Study : Testing ================= Contingency Table ================= Pheno Type ---------------- Col(wt) ---------------- 1(1) 2(0) TOTAL Case : 16 32 48 Control : 0 64 64 -- TOTAL : 16 96 112 ================= Quantitative Table ================= CoVar Mean ---------------- Col(wt) ---------------- 1(1) 2(0) Row Total CoVar-0 : 1.975385 2.157614 4.132998 -- Col TOTAL : 1.975385 2.157614 4.132998 Chi-squared : 2000 / 2000 total statistics calculated Observed statistic : 24.888889 Empirical p-value : 0.001 Odds Ratios, 2-Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 1v2:- Empirical p-value : 1v2:0.002 Empirical Confidence Intervals : (-, -) Quantitative, Two Tailed Test : 2000 / 2000 total statistics calculated Observed statistic : 1v2:-1.002694 Empirical p-value : 1v2:0.324 ________________________________________________________________ *** Analysis 8 *** Loci : ALL MARKERS Model : Hap 3 Rec REV Type : Genotype *** Study : Testing ================= Contingency Table ================= Pheno Type ---------------- Col(wt) ---------------- 1(1) 2(0) TOTAL Case : 0 48 48 Control : 0 64 64 -- TOTAL : 0 112 112 ================= Quantitative Table ================= CoVar Mean ---------------- Col(wt) ---------------- 1(1) 2(0) Row Total CoVar-0 : 0 2.134158 2.134158 -- Col TOTAL : 0 2.134158 2.134158 Chi-squared : 0 / 2000 total statistics calculated Observed statistic : WARNING: row or column sum equals zero, **test** has not been performed. Empirical p-value : - Odds Ratios, 2-Tailed Test : 1063 / 2000 total statistics calculated Observed statistic : 1v2:- Empirical p-value : 1v2:- Empirical Confidence Intervals : (-, -) Warning : 95% CI is uninformative, likely due to sparse data or insufficient simulations Quantitative, Two Tailed Test : 316 / 2000 total statistics calculated Observed statistic : 1v2:- Empirical p-value : 1v2:- ________________________________________________________________ *** Analysis 9 *** Loci : ALL MARKERS Model : Hap3 Additive R Type : Genotype *** Study : Testing ================= Contingency Table ================= Pheno Type ---------------- Col(wt) ---------------- 1(2) 2(1) 3(0) TOTAL Case : 0 16 32 48 Control : 0 0 64 64 -- TOTAL : 0 16 96 112 ================= Quantitative Table ================= CoVar Mean ---------------- Col(wt) ---------------- 1(2) 2(1) 3(0) Row Total CoVar-0 : 0 1.975385 2.157614 4.132998 -- Col TOTAL : 0 1.975385 2.157614 4.132998 Chi-squared : 0 / 2000 total statistics calculated Observed statistic : WARNING: row or column sum equals zero, **test** has not been performed. Empirical p-value : - Chi-squared Trend : 0 / 2000 total statistics calculated Observed statistic : WARNING: row or column sum equals zero, **test** has not been performed. Empirical p-value : - Odds Ratios, 2-Tailed Test : 1063 / 2000, 2000 / 2000 total statistics calculated Observed statistic : 1v3:- 2v3:- Empirical p-value : 1v3:- 2v3:0.002 Empirical Confidence Intervals : (-, -) (-, -) Warning : 95% CI is uninformative, likely due to sparse data or insufficient simulations Quantitative, Two Tailed Test : 316 / 2000, 2000 / 2000 total statistics calculated Observed statistic : 1v3:- 2v3:-1.002694 Observed Overall Statistic : - Empirical p-value : 1v3:- 2v3:0.3245 Empirical Overall p-value : - Elapse Time : 0 h : 4 m : 46 s ```