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 mr1076 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
vg0719007567 sf0719006574 7 19007567 2.21E-13 2.47E-11
vg0719001862 sf0719000869 7 19001862 1.98E-12 6.29E-12
vg0717197101 sf0717196108 7 17197101 1.23E-10 1.92E-08
vg0719140489 sf0719139496 7 19140489 1.96E-10 2.69E-07
vg0216351953 sf0216346083 2 16351953 4.33E-10 1.82E-06
vg1201545939 sf1201544939 12 1545939 2.05E-09 1.35E-07
vg0429343347 sf0429158213 4 29343347 2.96E-09 3.50E-07
vg0221853596 sf0221847727 2 21853596 1.77E-08 1.31E-06
vg0502193438 sf0502193413 5 2193438 1.24E-07 3.40E-06
vg0718924188 sf0718923195 7 18924188 2.15E-06 1.96E-07
vg1008804375 sf1008733237 10 8804375 2.64E-06 4.70E-06
vg1210130843 sf1210128254 12 10130843 3.24E-06 NA
vg0100920559 sf0100919559 1 920559 NA 9.60E-07
vg1009450763 sf1009379584 10 9450763 NA 2.50E-06
vg0504291251 sf0504291228 5 4291251 NA 2.84E-06