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 mr1065 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
vg0610559165 sf0610558166 6 10559165 3.28E-50 1.46E-28
vg0610566084 sf0610565085 6 10566084 8.82E-48 6.45E-28
vg0610774959 sf0610773960 6 10774959 1.17E-35 9.34E-22
vg0610418906 sf0610417907 6 10418906 1.37E-26 1.31E-14
vg0610683043 sf0610682044 6 10683043 1.87E-20 1.22E-14
vg0616119655 sf0616118657 6 16119655 3.17E-20 4.45E-06
vg0610874933 sf0610873934 6 10874933 5.40E-20 1.45E-10
vg0610442278 sf0610441279 6 10442278 6.11E-20 1.23E-15
vg0617383481 sf0617382484 6 17383481 1.34E-19 4.66E-07
vg0610644236 sf0610643237 6 10644236 6.74E-17 3.43E-11
vg0610148252 sf0610147253 6 10148252 6.18E-15 1.15E-09
vg0610152420 sf0610151421 6 10152420 1.87E-13 1.97E-08
vg0614785443 sf0614784444 6 14785443 2.23E-13 2.01E-07
vg0611561420 sf0611560421 6 11561420 2.27E-13 1.05E-07
vg0610435285 sf0610434286 6 10435285 1.20E-12 4.00E-09
vg0611471474 sf0611470475 6 11471474 3.82E-12 3.02E-08
vg0611953873 sf0611952874 6 11953873 2.21E-10 1.76E-06
vg0726451328 sf0726450334 7 26451328 8.66E-10 1.79E-06
vg0611649853 sf0611648854 6 11649853 3.18E-09 2.92E-07
vg0610105888 sf0610104889 6 10105888 NA 1.55E-07
vg0226057933 sf0226052064 2 26057933 NA 6.35E-07
vg0611255073 sf0611254074 6 11255073 NA 7.17E-07
vg0408367382 sf0408362656 4 8367382 NA 9.77E-07
vg0612105145 sf0612104146 6 12105145 NA 1.45E-06
vg0713349047 sf0713348054 7 13349047 NA 2.11E-06