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 mr1337 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
vg0607991416 sf0607990417 6 7991416 2.20E-09 6.32E-08
vg0726597617 sf0726596623 7 26597617 4.00E-08 1.45E-06
vg0424926413 sf0424741274 4 24926413 2.38E-07 1.88E-06
vg1106552757 sf1106548510 11 6552757 2.95E-07 4.38E-06
vg0421020772 sf0420848825 4 21020772 2.97E-07 6.09E-07
vg0421031215 sf0420859268 4 21031215 3.45E-07 8.92E-07
vg0704864945 sf0704863946 7 4864945 3.76E-07 4.96E-08
vg0416747657 sf0416575701 4 16747657 1.12E-06 6.84E-07
vg0516508609 sf0516451091 5 16508609 5.20E-06 3.79E-07
vg0232755756 sf0232749887 2 32755756 7.61E-06 3.95E-06
vg1224447613 sf1224414066 12 24447613 7.93E-06 5.40E-07
vg0421384856 sf0421212909 4 21384856 NA 1.98E-06
vg0607659813 sf0607658814 6 7659813 NA 2.35E-06
vg0420718113 sf0420546156 4 20718113 NA 2.83E-06