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 mr1921 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
vg0205284798 sf0205284796 2 5284798 5.89E-30 1.93E-15
vg0205301629 sf0205301628 2 5301629 5.07E-29 1.65E-15
vg0328102373 sf0328095427 3 28102373 3.72E-16 NA
vg0220779349 sf0220773481 2 20779349 6.72E-16 NA
vg0208279406 sf0208279405 2 8279406 1.60E-15 NA
vg0306236476 sf0306235476 3 6236476 2.04E-15 NA
vg0221694296 sf0221688427 2 21694296 1.12E-14 1.59E-06
vg0819860953 sf0819858240 8 19860953 2.53E-13 3.32E-06
vg0819137940 sf0819135227 8 19137940 2.96E-12 NA
vg0805872876 sf0805871879 8 5872876 6.11E-12 3.43E-06
vg1214615131 sf1214612471 12 14615131 1.27E-11 2.66E-06
vg1215647530 sf1215644827 12 15647530 4.92E-11 6.90E-06
vg0205284069 sf0205284067 2 5284069 NA 2.79E-09