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 mr1844 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
vg1224912536 sf1224878990 12 24912536 4.74E-15 NA
vg0400611332 sf0400610332 4 611332 2.01E-14 NA
vg0107825185 sf0107824185 1 7825185 7.45E-14 NA
vg1019886882 sf1019815382 10 19886882 1.48E-13 NA
vg0502284179 sf0502284154 5 2284179 1.58E-13 NA
vg0610480987 sf0610479988 6 10480987 4.06E-13 NA
vg0719334703 sf0719333710 7 19334703 5.48E-13 5.77E-07
vg0719511488 sf0719510495 7 19511488 9.92E-13 6.40E-07
vg0335925270 sf0335918139 3 35925270 7.92E-12 3.57E-07
vg0316249445 sf0316248093 3 16249445 NA 1.72E-07
vg0335796573 sf0335789442 3 35796573 NA 3.63E-07
vg0815304114 sf0815301400 8 15304114 NA 5.57E-07
vg0610468826 sf0610467827 6 10468826 NA 2.49E-06
vg0317916681 sf0317915463 3 17916681 NA 2.82E-06
vg0904010040 sf0904009040 9 4010040 NA 3.13E-06
vg0142100802 sf0142099759 1 42100802 NA 3.87E-06