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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Haplotype Analysis:

Haplotypes with frequency <0.03 are ignored.
Loci chosen for haplotype analysis: rs776746, rs2242480, rs4646437, rs1057868, rs2276707, rs227707, rs6785049, rs1523127, rs2257401, rs10211, rs12360

Haplotype	Case(freq)	Control(freq)	Chi²	Fisher's p	Pearson's p	OR [95% CI]
CCGTCAAAGTA	18(0.095)	18(0.096)	0.007	0.999	0.928	0.969 [0.489~1.919]
CCGCCAAAGTA	23(0.122)	17(0.091)	0.814	0.408	0.366	1.352 [0.7~2.612]
TTACTAGACCG	14(0.074)	10(0.053)	0.591	0.53	0.441	1.386 [0.601~3.194]
CCGCTAGAGTA	18(0.095)	26(0.139)	1.888	0.202	0.169	0.642 [0.341~1.211]
TTACCAAACCG	8(0.042)	4(0.021)	1.258	0.381	0.262	1.98 [0.587~6.68]
CCGTTAGAGTA	12(0.063)	8(0.043)	0.724	0.493	0.394	1.485 [0.594~3.71]
CCATCAAAGTA	3(0.015)	9(0.048)	3.266	0.083	0.07	0.314 [0.083~1.177]

Global result:
Total control=104, total case=107.
Global Chi² is 8.073, Fisher's p is NA, Pearson's p is 0.232.

Linkage Disequilibrium Analysis:

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Results export to excel

Haplotype Analysis:

Linkage Disequilibrium Analysis:

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Results

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