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 mr1163 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
vg0433811482 sf0433626370 4 33811482 2.95E-14 1.29E-07
vg0526919176 sf0526856533 5 26919176 9.46E-13 3.24E-06
vg1218097413 sf1218068849 12 18097413 1.50E-12 NA
vg0139256874 sf0139255831 1 39256874 1.72E-12 4.81E-06
vg0227395695 sf0227389826 2 27395695 1.84E-12 9.53E-06
vg0211579446 sf0211579442 2 11579446 1.38E-10 4.22E-06
vg1118675422 sf1118209230 11 18675422 1.67E-09 2.37E-06