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 mr1502 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
vg1121844671 sf1121378548 11 21844671 1.36E-09 NA
vg0413415787 sf0413406501 4 13415787 4.35E-09 NA
vg0315756494 sf0315755141 3 15756494 1.20E-08 NA
vg1000843357 sf1000842333 10 843357 1.24E-08 NA
vg0113615431 sf0113614405 1 13615431 3.00E-08 8.21E-06
vg0221870781 sf0221864912 2 21870781 2.11E-07 1.05E-06
vg0315837144 sf0315835791 3 15837144 2.99E-06 NA