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 mr1698 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
vg0200799836 sf0200799836 2 799836 2.48E-29 5.35E-07
vg0121628144 sf0121627099 1 21628144 3.04E-29 2.36E-08
vg1121988122 sf1121521993 11 21988122 9.56E-28 1.26E-08
vg0420291464 sf0420119509 4 20291464 3.79E-27 4.20E-07
vg1119464721 sf1118998409 11 19464721 1.17E-26 9.49E-08
vg1119344463 sf1118878151 11 19344463 6.26E-26 7.29E-08
vg0608288723 sf0608287724 6 8288723 2.32E-24 3.13E-06
vg0404607386 sf0404602989 4 4607386 7.10E-24 1.32E-06
vg0608186679 sf0608185680 6 8186679 1.46E-22 NA
vg1003331343 sf1003330320 10 3331343 2.85E-21 1.21E-06
vg0405876106 sf0405871547 4 5876106 NA 1.97E-07
vg0305186351 sf0305185351 3 5186351 NA 1.27E-06
vg1122183779 sf1121717650 11 22183779 NA 2.13E-06
vg0404794664 sf0404790103 4 4794664 NA 2.69E-06
vg0726372325 sf0726371331 7 26372325 NA 2.75E-06
vg0400063937 sf0400062937 4 63937 NA 2.88E-06
vg1122003053 sf1121536924 11 22003053 NA 3.39E-06
vg0323085855 sf0323084343 3 23085855 NA 3.41E-06
vg0110864670 sf0110863646 1 10864670 NA 3.53E-06
vg0400114187 sf0400113187 4 114187 NA 6.42E-06