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 mr1418 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
vg1218087170 sf1218058606 12 18087170 5.06E-11 3.39E-07
vg1117584893 sf1117118750 11 17584893 1.10E-08 NA
vg1002090281 sf1002089258 10 2090281 1.50E-08 NA
vg0619934912 sf0619933915 6 19934912 3.84E-08 NA
vg1022649587 sf1022578061 10 22649587 3.87E-08 NA
vg0104271546 sf0104270546 1 4271546 2.26E-07 2.77E-06
vg1009009289 sf1008938150 10 9009289 NA 2.39E-06
vg0118091762 sf0118090716 1 18091762 NA 3.97E-06