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 mr1622 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
vg0515672827 sf0515615368 5 15672827 2.55E-09 1.22E-07
vg0820443724 sf0820441011 8 20443724 2.58E-09 2.70E-07
vg0820117988 sf0820115275 8 20117988 2.60E-09 5.89E-08
vg0820047628 sf0820044915 8 20047628 3.23E-09 5.32E-08
vg0108674689 sf0108673689 1 8674689 3.68E-08 7.41E-07
vg1209461512 sf1209458921 12 9461512 3.87E-08 1.28E-06
vg0914108391 sf0914107390 9 14108391 9.71E-08 7.23E-06
vg1000734007 sf1000732983 10 734007 5.47E-07 2.61E-06
vg0728927679 sf0728926687 7 28927679 6.06E-07 3.74E-07
vg0207916446 sf0207916445 2 7916446 8.69E-07 2.42E-06
vg1022721487 sf1022649961 10 22721487 9.34E-07 4.10E-06
vg0525579310 sf0525516731 5 25579310 1.31E-06 4.43E-06
vg0214173791 sf0214167921 2 14173791 2.19E-06 5.65E-07
vg0223641214 sf0223635345 2 23641214 NA 1.17E-06
vg0617484074 sf0617483077 6 17484074 NA 3.83E-06
vg1004719297 sf1004735834 10 4719297 NA 9.08E-06