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 mr1528 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
vg0816082795 sf0816080081 8 16082795 7.10E-08 7.14E-08
vg0622509231 sf0622508234 6 22509231 2.34E-07 3.42E-06
vg1010265724 sf1010194545 10 10265724 2.60E-07 2.05E-07
vg0804827547 sf0804826550 8 4827547 4.33E-07 7.68E-07
vg0710361771 sf0710360777 7 10361771 2.15E-06 4.03E-06
vg0817027394 sf0817024680 8 17027394 6.39E-06 1.92E-06
vg0516131571 sf0516074055 5 16131571 7.78E-06 1.93E-06
vg0408103365 sf0408098639 4 8103365 NA 1.45E-06
vg0713573114 sf0713572121 7 13573114 NA 2.91E-06
vg0114137072 sf0114136046 1 14137072 NA 3.60E-06
vg0611626951 sf0611625952 6 11626951 NA 3.76E-06
vg0813025998 sf0813023823 8 13025998 NA 4.13E-06