Results

Please cite:

Shen, J. et al. SHEsisPlus, a toolset for genetic studies on polyploid species. Sci. Rep. 6, 24095; doi: 10.1038/srep24095 (2016).

Shi, Y. et al. SHEsis, a powerful software platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci. Cell Res. 15, 97–98; doi: 10.1038/sj.cr.7290272 (2005).

Li, Z. et al. A partition-ligation-combination-subdivision EM algorithm for haplotype inference with multiallelic markers. Cell Res. 19, 519–523; doi: 10.1038/cr.2009.33 (2009).

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Single Locus Association Test (Binary phenotype):

Alleles:

SNP	Call rate	Chi²	Pearson's p	Fisher's p	OR [95% CI]	Holm	SidakSS	SidakSD	FDR_BH	FDR_BY	Detail
rs1800497	1	0.04	0.839	0.901	1.051 [0.646~1.711]	1	0.999	0.974	0.918	1	G A Case 73(0.579) 53(0.42) Control 84(0.591) 58(0.408)
rs4633	1	0.446	0.504	0.555	1.217 [0.682~2.171]	1	0.999	0.939	0.693	1	C T Case 96(0.761) 30(0.238) Control 113(0.795) 29(0.204)
rs4680	1	0.276	0.598	0.66	1.166 [0.656~2.072]	1	0.999	0.939	0.732	1	G A Case 96(0.761) 30(0.238) Control 112(0.788) 30(0.211)
rs8192620	1	5.415	0.019	0.026	0.538 [0.318~0.909]	0.199	0.198	0.182	0.109	0.331	C T Case 32(0.253) 94(0.746) Control 55(0.387) 87(0.612)
rs482951	1	2.27	0.131	0.22	NA [NA~NA]	0.714	0.788	0.532	0.207	0.625	G C Case 124(0.984) 2(0.015) Control 142(1) 0(0)
rs2280506	1	2.428	0.119	0.128	1.54 [0.893~2.659]	0.714	0.752	0.532	0.207	0.625	C T Case 39(0.309) 87(0.69) Control 32(0.225) 110(0.774)
rs2280507	1	3.37	0.066	0.072	1.665 [0.963~2.878]	0.596	0.53	0.46	0.162	0.491	C T Case 86(0.682) 40(0.317) Control 111(0.781) 31(0.218)
rs6744273	1	3.371	0.066	0.074	1.658 [0.964~2.851]	0.596	0.529	0.46	0.162	0.491	G A Case 41(0.325) 85(0.674) Control 32(0.225) 110(0.774)
rs13538	1	NA	NA	NA	NA [NA~NA]	NA	NA	NA	NA	NA	A Case 126(1) Control 142(1)
rs5751876	1	3.193	0.073	0.086	1.551 [0.957~2.515]	0.596	0.57	0.46	0.162	0.491	C T Case 67(0.531) 59(0.468) Control 60(0.422) 82(0.577)
rs11030104	1	0.01	0.918	1	0.975 [0.601~1.579]	1	0.999	0.974	0.918	1	G A Case 70(0.555) 56(0.444) Control 78(0.549) 64(0.45)

Genotypes:

SNP	Chi²	Pearson's p	Fisher's p	Holm	SidakSS	SidakSD	FDR_BH	FDR_BY	Detail
rs1800497	0.084	0.958	0.971	1	0.999	0.958	0.958	1	G/G A/A G/A Case 20(0.317) 10(0.158) 33(0.523) Control 23(0.323) 10(0.14) 38(0.535)
rs4633	1.566	0.456	0.498	1	0.998	0.815	0.502	1	C/C C/T T/T Case 39(0.619) 18(0.285) 6(0.095) Control 45(0.633) 23(0.323) 3(0.042)
rs4680	1.686	0.43	0.441	1	0.997	0.815	0.502	1	G/G A/A G/A Case 39(0.619) 6(0.095) 18(0.285) Control 44(0.619) 3(0.042) 24(0.338)
rs8192620	5.159	0.075	0.082	0.757	0.579	0.545	0.33	0.998	C/T T/T C/C Case 20(0.317) 37(0.587) 6(0.095) Control 31(0.436) 28(0.394) 12(0.169)
rs482951	2.288	0.13	0.219	1	0.784	0.715	0.33	0.998	G/G G/C Case 61(0.968) 2(0.031) Control 71(1) 0(0)
rs2280506	2.55	0.279	0.273	1	0.972	0.743	0.384	1	C/T T/T C/C Case 27(0.428) 30(0.476) 6(0.095) Control 26(0.366) 42(0.591) 3(0.042)
rs2280507	3.426	0.18	0.184	1	0.887	0.743	0.33	0.998	C/T T/T C/C Case 28(0.444) 6(0.095) 29(0.46) Control 25(0.352) 3(0.042) 43(0.605)
rs6744273	3.534	0.17	0.177	1	0.872	0.743	0.33	0.998	G/A A/A G/G Case 27(0.428) 29(0.46) 7(0.111) Control 26(0.366) 42(0.591) 3(0.042)
rs13538	NA	NA	NA	NA	NA	NA	NA	NA	A/A Case 63(1) Control 71(1)
rs5751876	3.713	0.156	0.179	1	0.845	0.743	0.33	0.998	C/C T/T C/T Case 18(0.285) 14(0.222) 31(0.492) Control 11(0.154) 22(0.309) 38(0.535)
rs11030104	2.942	0.229	0.234	1	0.943	0.743	0.36	1	G/A G/G A/A Case 34(0.539) 18(0.285) 11(0.174) Control 28(0.394) 25(0.352) 18(0.253)

Hardy-Weinberg Equilibrium Test:

SNP	Chi² in case	Pearson's p in case	Fisher's p in case	Chi² in ctrl	Pearson's p in ctrl	Fisher's p in ctrl	Chi² in both	Pearson's p in both	Fisher's p in both
rs1800497	0.351	0.838	0.913	0.821	0.663	0.894	1.13	0.568	0.84
rs4633	2.844	0.241	0.469	8.00e-04	0.999	1	1.589	0.451	0.629
rs4680	2.844	0.241	0.469	0.014	0.992	1	1.288	0.524	0.659
rs8192620	1.658	0.436	0.702	0.454	0.796	0.922	2.335	0.311	0.607
rs482951	5.16e-04	0.981	1	0	1	1	1.13e-04	0.991	0.999
rs2280506	4.43e-04	0.999	1	0.169	0.918	0.955	0.032	0.984	1
rs2280507	0.041	0.979	1	0.071	0.965	1	0.032	0.984	1
rs6744273	0.035	0.982	1	0.169	0.918	0.955	6.35e-04	0.999	1
rs13538	0	1	NA	0	1	NA	0	1	NA
rs5751876	0.008	0.995	1	0.664	0.717	0.897	0.143	0.93	0.96
rs11030104	0.543	0.762	0.914	2.941	0.229	0.434	0.555	0.757	0.839

Haplotype Analysis:

Haplotypes with frequency <0.03 are ignored.
Loci chosen for haplotype analysis: rs1800497, rs4633, rs4680, rs8192620, rs482951, rs2280506, rs2280507, rs6744273, rs13538, rs5751876, rs11030104

Haplotype	Case(freq)	Control(freq)	Chi²	Fisher's p	Pearson's p	OR [95% CI]	Holm	SidakSS	SidakSD	FDR_BH	FDR_BY
GCGTGTCAACA	5(0.039)	4(0.028)	0.272	0.738	0.601	1.425 [0.374~5.429]	1	1	0.99	0.651	1
ACGTGTCAACG	7(0.055)	7(0.049)	0.052	0.999	0.818	1.134 [0.386~3.328]	1	1	0.996	0.834	1
ACGTGTCAATA	7(0.055)	4(0.028)	1.272	0.357	0.259	2.029 [0.579~7.102]	1	0.999	0.963	0.321	1
GTACGTCAATA	6(0.047)	4(0.028)	0.703	0.523	0.401	1.725 [0.475~6.257]	1	0.999	0.99	0.455	1
ACGTGTCAACA	11(0.087)	14(0.098)	0.1	0.834	0.751	0.874 [0.381~2.003]	1	1	0.996	0.797	1
GCGTGTCAATG	9(0.071)	9(0.063)	0.069	0.811	0.792	1.136 [0.436~2.959]	1	1	0.996	0.824	1
GCGTGTCAACG	7(0.055)	8(0.056)	7.74e-04	0.999	0.977	0.985 [0.346~2.798]	1	1	0.996	0.977	1
ACGCGTCAATA	3(0.023)	6(0.042)	0.699	0.507	0.402	0.552 [0.135~2.258]	1	0.999	0.99	0.455	1
GCGTGCTGACG	11(0.087)	3(0.021)	5.904	0.024	0.015	4.431 [1.207~16.266]	0.196	0.546	0.179	0.019	0.089
ACGTGTCAATG	6(0.047)	10(0.07)	0.618	0.454	0.431	0.66 [0.232~1.87]	1	0.999	0.99	0.477	1
GCGCGTCAATG	3(0.023)	6(0.042)	0.699	0.507	0.402	0.552 [0.135~2.258]	1	0.999	0.99	0.455	1
GCGTGTCAATA	3(0.023)	7(0.049)	1.207	0.343	0.271	0.47 [0.119~1.859]	1	0.999	0.963	0.328	1
GTACGTCAATG	1(0.007)	8(0.056)	4.819	0.038	0.028	0.134 [0.016~1.086]	0.337	0.773	0.29	0.035	0.161

Global result:
Total control=71, total case=63.
Global Chi² is 15.722, Fisher's p is NA, Pearson's p is 0.204.

Linkage Disequilibrium Analysis:

D'

R²

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