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 mr1026 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
vg0420116884 sf0419944922 4 20116884 4.12E-10 NA
vg0141861461 sf0141860418 1 41861461 3.98E-09 NA
vg1001361549 sf1001360526 10 1361549 4.70E-09 NA
vg0709675339 sf0709674345 7 9675339 5.33E-09 2.87E-06
vg0709672722 sf0709671728 7 9672722 8.37E-09 2.35E-06
vg1109241491 sf1109236068 11 9241491 9.55E-09 8.05E-06
vg0805104629 sf0805103632 8 5104629 1.70E-08 NA
vg0709672762 sf0709671768 7 9672762 2.51E-08 1.77E-06
vg1002794424 sf1002793401 10 2794424 2.77E-07 NA