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 mr1874 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
vg0825036742 sf0825034028 8 25036742 1.39E-55 6.40E-31
vg0825246180 sf0825243466 8 25246180 3.74E-21 8.56E-11
vg0804123261 sf0804122264 8 4123261 4.76E-19 NA
vg0702257412 sf0702256413 7 2257412 1.21E-18 NA
vg0825569796 sf0825567082 8 25569796 3.74E-18 1.44E-12
vg1009610847 sf1009539668 10 9610847 2.34E-17 5.50E-07
vg0825068464 sf0825065750 8 25068464 NA 2.35E-16
vg0825559450 sf0825556736 8 25559450 NA 2.57E-07
vg0825502549 sf0825499835 8 25502549 NA 1.09E-06
vg0620360503 sf0620359506 6 20360503 NA 2.69E-06
vg0324122964 sf0324121043 3 24122964 NA 2.96E-06
vg0208721652 sf0208721651 2 8721652 NA 3.56E-06
vg0529452069 sf0529389424 5 29452069 NA 3.76E-06
vg0210157400 sf0210157398 2 10157400 NA 4.17E-06