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 mr1404 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
vg0719007567 sf0719006574 7 19007567 7.16E-30 6.39E-23
vg0719207675 sf0719206682 7 19207675 3.32E-17 8.68E-15
vg0719136416 sf0719135423 7 19136416 1.38E-14 1.35E-11
vg1201654412 sf1201653412 12 1654412 5.57E-11 7.87E-08
vg0707711771 sf0707710776 7 7711771 1.97E-09 2.48E-06
vg0718886158 sf0718885165 7 18886158 2.19E-09 3.52E-07
vg0719005656 sf0719004663 7 19005656 3.95E-09 4.82E-06
vg0304916753 sf0304915755 3 4916753 6.60E-09 4.47E-06
vg0719127230 sf0719126237 7 19127230 1.34E-08 1.07E-07
vg0719016083 sf0719015090 7 19016083 3.09E-08 2.37E-06
vg0336302800 sf0336295670 3 36302800 3.27E-08 7.04E-07
vg1202542327 sf1202541329 12 2542327 1.95E-07 NA
vg0719725023 sf0719724030 7 19725023 4.60E-07 2.81E-06
vg0719443406 sf0719442413 7 19443406 1.22E-06 4.39E-06
vg0718985954 sf0718984961 7 18985954 8.10E-06 1.07E-08
vg0118254834 sf0118253788 1 18254834 NA 3.76E-06