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 mr1788 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
vg0906631032 sf0906630032 9 6631032 2.39E-09 2.78E-07
vg1124303986 sf1123837856 11 24303986 6.32E-09 NA
vg1122032445 sf1121566316 11 22032445 1.29E-08 NA
vg0710080818 sf0710079824 7 10080818 6.49E-08 6.66E-06
vg0805548082 sf0805547085 8 5548082 6.78E-08 NA
vg0500157710 sf0500157710 5 157710 2.39E-07 3.82E-06
vg0814295706 sf0814292992 8 14295706 3.03E-06 8.24E-06
vg0433421279 sf0433236168 4 33421279 NA 3.07E-07
vg0206119753 sf0206119753 2 6119753 NA 1.97E-06
vg0510324989 sf0510324918 5 10324989 NA 3.44E-06
vg0142377442 sf0142376398 1 42377442 NA 4.89E-06