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 mr1941 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
vg0820969276 sf0820966563 8 20969276 3.03E-07 3.03E-07
vg1210189485 sf1210186896 12 10189485 3.68E-07 3.68E-07
vg0820974361 sf0820971648 8 20974361 4.82E-07 4.82E-07
vg0431411704 sf0431226602 4 31411704 9.57E-07 9.57E-07
vg1219591736 sf1219563206 12 19591736 1.32E-06 1.32E-06
vg0229918162 sf0229912293 2 29918162 1.67E-06 1.67E-06
vg0709984451 sf0709983457 7 9984451 2.39E-06 2.39E-06
vg1107375253 sf1107370998 11 7375253 2.79E-06 2.79E-06
vg0719981901 sf0719980908 7 19981901 3.21E-06 3.21E-06
vg1214822308 sf1214819649 12 14822308 3.23E-06 3.23E-06
vg0131880868 sf0131879824 1 31880868 4.39E-06 4.39E-06
vg1104990849 sf1104986660 11 4990849 4.41E-06 4.41E-06
vg1009413787 sf1009342608 10 9413787 4.85E-06 4.85E-06