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 mr1584 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
vg1209388336 sf1209385745 12 9388336 9.84E-09 9.83E-09
vg1215481439 sf1215478736 12 15481439 9.61E-08 9.61E-08
vg0905282574 sf0905281574 9 5282574 1.11E-07 1.11E-07
vg1122981002 sf1122514873 11 22981002 2.21E-07 2.21E-07
vg1101210653 sf1101209654 11 1210653 3.50E-07 3.50E-07
vg0411353933 sf0411344636 4 11353933 4.84E-07 4.84E-07
vg0801862911 sf0801861914 8 1862911 5.48E-07 5.48E-07
vg0717726967 sf0717725974 7 17726967 5.72E-07 5.72E-07
vg1212601474 sf1212598813 12 12601474 1.15E-06 1.15E-06
vg1205317498 sf1205316484 12 5317498 1.82E-06 1.82E-06
vg0714855686 sf0714854693 7 14855686 2.19E-06 2.19E-06
vg0909184456 sf0909183455 9 9184456 2.58E-06 2.58E-06
vg1214822308 sf1214819649 12 14822308 3.57E-06 3.57E-06
vg1209224096 sf1209221505 12 9224096 3.93E-06 3.93E-06