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 mr1067 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
vg1123222536 sf1122756407 11 23222536 2.54E-10 2.54E-10
vg0431633623 sf0431448516 4 31633623 4.20E-09 4.19E-09
vg0124173863 sf0124172819 1 24173863 6.69E-09 6.69E-09
vg1220092619 sf1220064061 12 20092619 1.54E-08 1.54E-08
vg0820198596 sf0820195883 8 20198596 1.95E-08 1.95E-08
vg0616129303 sf0616128305 6 16129303 1.95E-08 1.95E-08
vg0521569979 sf0521507420 5 21569979 2.26E-08 2.26E-08
vg0619272417 sf0619258272 6 19272417 9.36E-08 9.36E-08
vg1209876216 sf1209873626 12 9876216 1.66E-07 1.66E-07
vg0105393860 sf0105392860 1 5393860 2.34E-07 2.33E-07
vg0619658716 sf0619657719 6 19658716 4.94E-07 4.94E-07
vg1004596366 sf1004612904 10 4596366 5.72E-07 5.72E-07
vg0916734760 sf0916733759 9 16734760 7.62E-07 7.62E-07
vg0209656030 sf0209656028 2 9656030 8.55E-07 8.55E-07
vg0324202574 sf0324200653 3 24202574 9.41E-07 9.41E-07
vg0712941986 sf0712940993 7 12941986 1.15E-06 1.15E-06
vg0600569739 sf0600568740 6 569739 1.31E-06 1.31E-06
vg0433192266 sf0433007154 4 33192266 1.79E-06 1.79E-06
vg1206256269 sf1206255159 12 6256269 2.09E-06 2.09E-06
vg0712599200 sf0712598207 7 12599200 2.78E-06 2.78E-06