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 mr1610 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
vg0217134280 sf0217128410 2 17134280 1.30E-34 1.41E-18
vg0217133783 sf0217127913 2 17133783 1.82E-27 4.01E-16
vg0216977757 sf0216971887 2 16977757 8.31E-21 1.98E-17
vg0216980822 sf0216974952 2 16980822 1.22E-20 3.85E-17
vg1220336354 sf1220307796 12 20336354 1.43E-18 2.58E-06
vg0217940314 sf0217934445 2 17940314 1.77E-17 3.22E-08
vg1015182556 sf1015111324 10 15182556 6.15E-17 NA
vg0513504499 sf0513447046 5 13504499 1.82E-15 NA
vg0216447677 sf0216441807 2 16447677 2.69E-14 2.45E-08
vg1003674168 sf1003673145 10 3674168 5.22E-14 1.86E-06
vg0218635577 sf0218629708 2 18635577 7.63E-13 4.60E-06
vg0217474288 sf0217468418 2 17474288 NA 2.33E-09
vg0217027791 sf0217021921 2 17027791 NA 2.71E-08
vg0217459136 sf0217453266 2 17459136 NA 4.45E-08
vg0421568928 sf0421396978 4 21568928 NA 9.86E-07
vg0421600078 sf0421428128 4 21600078 NA 1.03E-06
vg0217637634 sf0217631764 2 17637634 NA 1.81E-06
vg0421466152 sf0421294203 4 21466152 NA 2.39E-06
vg0217805111 sf0217799242 2 17805111 NA 2.91E-06
vg0430881589 sf0430696467 4 30881589 NA 4.37E-06
vg0217461026 sf0217455156 2 17461026 NA 4.38E-06
vg0525001887 sf0524939302 5 25001887 NA 8.34E-06