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 mr1484 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
vg1125085416 sf1124619256 11 25085416 1.36E-10 3.54E-09
vg1124335549 sf1123869393 11 24335549 3.44E-10 3.67E-09
vg0815306355 sf0815303641 8 15306355 1.30E-09 2.83E-08
vg0314909213 sf0314907860 3 14909213 2.02E-08 3.11E-08
vg1125990989 sf1125519403 11 25990989 2.49E-08 3.18E-07
vg0815806693 sf0815803979 8 15806693 2.50E-08 2.94E-06
vg0814220352 sf0814217638 8 14220352 3.26E-08 6.79E-07
vg0815800560 sf0815797846 8 15800560 5.23E-08 7.59E-07
vg1104596397 sf1104592299 11 4596397 1.17E-07 9.27E-07
vg0715539794 sf0715538801 7 15539794 1.86E-07 4.96E-07
vg0811469683 sf0811468688 8 11469683 5.29E-07 1.84E-06
vg0811646982 sf0811645987 8 11646982 6.50E-07 3.99E-06
vg0526332116 sf0526269479 5 26332116 7.33E-07 5.31E-07
vg0208128713 sf0208128712 2 8128713 9.28E-07 1.98E-06
vg1214799098 sf1214796439 12 14799098 1.82E-06 2.69E-06
vg1124940229 sf1124474069 11 24940229 1.83E-06 2.55E-06
vg1214931700 sf1214929042 12 14931700 2.08E-06 1.67E-06
vg0526675403 sf0526612761 5 26675403 NA 2.47E-06