Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1151 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0822295827 sf0822293114 8 22295827 8.13E-17 1.89E-08
vg0822296656 sf0822293943 8 22296656 1.22E-16 1.68E-08
vg0822287446 sf0822284733 8 22287446 1.66E-16 3.81E-08
vg0220859237 sf0220853369 2 20859237 2.50E-16 3.48E-06
vg0220874371 sf0220868503 2 20874371 5.98E-16 2.22E-06
vg0103417456 sf0103416456 1 3417456 1.54E-15 NA
vg0725887430 sf0725886436 7 25887430 1.81E-15 NA
vg0434389908 sf0434204802 4 34389908 1.83E-15 NA
vg0800333217 sf0800332217 8 333217 1.81E-13 1.54E-06
vg0616930764 sf0616929767 6 16930764 8.26E-13 1.54E-06
vg0822299189 sf0822296476 8 22299189 1.32E-12 1.11E-07
vg0334370940 sf0334363810 3 34370940 NA 1.28E-09
vg0335925270 sf0335918139 3 35925270 NA 1.74E-08
vg0335435424 sf0335428293 3 35435424 NA 5.13E-08
vg0904010040 sf0904009040 9 4010040 NA 1.01E-07
vg0142100802 sf0142099759 1 42100802 NA 3.58E-07
vg0334413233 sf0334406103 3 34413233 NA 5.47E-07
vg0334779506 sf0334772376 3 34779506 NA 1.05E-06
vg0322467033 sf0322465522 3 22467033 NA 1.07E-06
vg0334290772 sf0334283642 3 34290772 NA 1.69E-06
vg0909468501 sf0909467500 9 9468501 NA 1.97E-06
vg1214134657 sf1214131997 12 14134657 NA 2.06E-06
vg0818200735 sf0818198022 8 18200735 NA 2.11E-06
vg0335186694 sf0335179563 3 35186694 NA 2.40E-06
vg0318065659 sf0318064441 3 18065659 NA 2.45E-06
vg1115981616 sf1115516488 11 15981616 NA 3.02E-06
vg0326004558 sf0326002578 3 26004558 NA 3.06E-06
vg0431474782 sf0431289680 4 31474782 NA 3.06E-06
vg0719508934 sf0719507941 7 19508934 NA 4.45E-06
vg0908388286 sf0908387286 9 8388286 NA 4.58E-06
vg0317321849 sf0317320659 3 17321849 NA 4.76E-06