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 mr1326 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
vg0103967221 sf0103966221 1 3967221 1.19E-16 NA
vg0103964702 sf0103963702 1 3964702 1.28E-16 NA
vg1022648377 sf1022576851 10 22648377 6.88E-16 NA
vg0620351584 sf0620350587 6 20351584 1.03E-15 NA
vg0504757167 sf0504757144 5 4757167 1.11E-15 NA
vg0919649275 sf0919648865 9 19649275 1.73E-15 NA
vg0900371978 sf0900370978 9 371978 2.12E-15 NA
vg0208609024 sf0208609023 2 8609024 NA 1.48E-06
vg1214701611 sf1214698952 12 14701611 NA 1.53E-06
vg0518984986 sf0518922470 5 18984986 NA 1.83E-06
vg1214644504 sf1214641844 12 14644504 NA 2.59E-06
vg1214644530 sf1214641870 12 14644530 NA 2.66E-06
vg1214380715 sf1214378056 12 14380715 NA 9.48E-06