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 mr1585 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
vg0325696417 sf0325694435 3 25696417 3.15E-49 2.97E-40
vg0400345487 sf0400344487 4 345487 1.67E-19 7.32E-12
vg1004789770 sf1004806307 10 4789770 1.92E-18 1.90E-12
vg1007920179 sf1007935789 10 7920179 7.74E-18 8.05E-09
vg1007924793 sf1007940403 10 7924793 1.06E-17 1.05E-09
vg0229389860 sf0229383991 2 29389860 2.75E-17 3.13E-09
vg0609841754 sf0609840755 6 9841754 4.15E-15 2.34E-11
vg1005573976 sf1005590514 10 5573976 6.60E-15 3.89E-10
vg1002067295 sf1002066272 10 2067295 8.92E-14 3.48E-08
vg0224013358 sf0224007489 2 24013358 4.75E-13 2.59E-08
vg0416712669 sf0416540713 4 16712669 1.10E-12 1.07E-08
vg1011003657 sf1010932477 10 11003657 1.28E-12 1.13E-08
vg0317037478 sf0317036352 3 17037478 1.58E-12 7.40E-08
vg1012888857 sf1012817672 10 12888857 4.16E-12 3.86E-10
vg0304791741 sf0304790743 3 4791741 7.21E-12 1.50E-08
vg0315592194 sf0315590841 3 15592194 9.59E-12 4.62E-08
vg0220327675 sf0220321807 2 20327675 1.02E-11 1.53E-08
vg0322796391 sf0322794880 3 22796391 1.98E-11 1.65E-09
vg0311067844 sf0311066562 3 11067844 5.04E-11 1.62E-08
vg0415028838 sf0415019552 4 15028838 6.66E-11 2.67E-08
vg0207824124 sf0207824123 2 7824124 2.77E-08 7.76E-09
vg1003305174 sf1003304151 10 3305174 3.56E-06 NA