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 mr1151 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
vg0110161014 sf0110159990 1 10161014 4.14E-07 4.14E-07
vg1004892287 sf1004908824 10 4892287 5.37E-07 5.37E-07
vg1004874392 sf1004890929 10 4874392 1.08E-06 1.08E-06
vg0110808194 sf0110807170 1 10808194 1.31E-06 1.31E-06
vg1004296464 sf1004313002 10 4296464 1.42E-06 1.42E-06
vg1207359848 sf1207357255 12 7359848 2.68E-06 2.68E-06
vg0103417456 sf0103416456 1 3417456 3.08E-06 3.08E-06
vg1212015428 sf1212012763 12 12015428 4.17E-06 4.17E-06
vg0235196559 sf0235190690 2 35196559 4.28E-06 4.28E-06
vg0126648826 sf0126647782 1 26648826 4.72E-06 4.72E-06