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 mr1244 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
vg0610566343 sf0610565344 6 10566343 3.63E-34 2.59E-20
vg0610566084 sf0610565085 6 10566084 1.44E-33 5.95E-20
vg0920309356 sf0920308875 9 20309356 3.89E-18 3.92E-10
vg0920309427 sf0920308946 9 20309427 7.59E-18 3.18E-10
vg0705277362 sf0705276363 7 5277362 1.16E-15 2.03E-07
vg0610736522 sf0610735523 6 10736522 3.99E-14 6.76E-06
vg0610126409 sf0610125410 6 10126409 2.35E-13 6.96E-07
vg0802717838 sf0802716841 8 2717838 2.85E-12 NA
vg0610116533 sf0610115534 6 10116533 6.79E-11 3.09E-10
vg0708597730 sf0708596735 7 8597730 3.07E-10 4.65E-06
vg0726491978 sf0726490984 7 26491978 5.58E-09 NA
vg0423902951 sf0423717810 4 23902951 1.84E-08 2.27E-07
vg0610419183 sf0610418184 6 10419183 3.62E-08 5.18E-07
vg0610072196 sf0610071197 6 10072196 4.10E-07 2.81E-08
vg0610429643 sf0610428644 6 10429643 NA 1.14E-06
vg0619240761 sf0619239764 6 19240761 NA 1.25E-06
vg0615850189 sf0615849191 6 15850189 NA 3.76E-06