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 mr1721 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
vg0708334737 sf0708333742 7 8334737 5.08E-57 9.29E-07
vg0322441125 sf0322439614 3 22441125 8.52E-56 NA
vg0318045543 sf0318044325 3 18045543 7.10E-55 NA
vg0501544813 sf0501544797 5 1544813 8.29E-55 NA
vg0704638016 sf0704637017 7 4638016 3.46E-54 NA
vg0304938695 sf0304937697 3 4938695 1.12E-53 1.42E-06
vg0804699109 sf0804698112 8 4699109 2.21E-50 8.96E-07
vg1001385051 sf1001384028 10 1385051 NA 3.31E-12
vg1001448127 sf1001447104 10 1448127 NA 3.70E-10
vg0720057906 sf0720056913 7 20057906 NA 1.39E-07
vg1001392057 sf1001391034 10 1392057 NA 1.18E-06
vg1001426279 sf1001425256 10 1426279 NA 1.80E-06
vg0421499528 sf0421327579 4 21499528 NA 4.07E-06