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 mr1154 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
vg1115487625 sf1115023938 11 15487625 9.61E-15 6.00E-09
vg1115480914 sf1115017227 11 15480914 3.40E-14 2.28E-10
vg1109787121 sf1109781698 11 9787121 2.66E-13 NA
vg1111902205 sf1111896522 11 11902205 4.07E-12 1.54E-08
vg0435342541 sf0435157422 4 35342541 1.24E-10 NA
vg1115413712 sf1114950024 11 15413712 2.81E-10 1.22E-10
vg1115387288 sf1114923600 11 15387288 5.84E-10 8.82E-11
vg1109779912 sf1109774489 11 9779912 1.35E-08 1.52E-06
vg1112708625 sf1112244946 11 12708625 1.39E-08 6.23E-08
vg0719006640 sf0719005647 7 19006640 7.98E-07 NA
vg1114444146 sf1113980463 11 14444146 1.05E-06 NA
vg0141149267 sf0141148224 1 41149267 3.54E-06 NA
vg0216528446 sf0216522576 2 16528446 3.72E-06 3.42E-06
vg0606957055 sf0606956056 6 6957055 NA 2.19E-06