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 mr1013 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
vg1209270443 sf1209267853 12 9270443 7.23E-11 3.80E-08
vg0433675778 sf0433490661 4 33675778 1.41E-10 4.49E-07
vg0526905981 sf0526843338 5 26905981 1.52E-10 1.68E-06
vg0304178129 sf0304177131 3 4178129 3.08E-10 9.22E-06
vg0433930554 sf0433745450 4 33930554 3.19E-10 6.28E-08
vg0111704491 sf0111703465 1 11704491 1.60E-09 9.43E-06
vg1114551548 sf1114087865 11 14551548 5.05E-09 1.50E-06
vg0225258958 sf0225253089 2 25258958 5.90E-09 1.60E-06
vg0224504649 sf0224498780 2 24504649 2.54E-08 4.22E-06
vg1118460774 sf1117994633 11 18460774 2.79E-08 1.26E-06
vg1203926835 sf1203925834 12 3926835 3.97E-08 NA
vg0522604659 sf0522542102 5 22604659 5.31E-08 7.19E-07
vg1208112458 sf1208109864 12 8112458 6.09E-08 1.49E-06
vg1006058550 sf1006075088 10 6058550 3.49E-07 4.57E-06
vg1009343932 sf1009272753 10 9343932 3.80E-07 1.54E-06