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 mr1934 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
vg0524494561 sf0524431982 5 24494561 7.27E-133 5.11E-29
vg0524484639 sf0524422060 5 24484639 7.46E-132 6.72E-30
vg0807294325 sf0807293330 8 7294325 3.64E-82 NA
vg0502008041 sf0502008023 5 2008041 4.04E-81 NA
vg0321280855 sf0321279365 3 21280855 4.31E-80 NA
vg0407876407 sf0407871675 4 7876407 9.08E-80 NA
vg0524738001 sf0524675422 5 24738001 NA 1.26E-19
vg1100143008 sf1100142009 11 143008 NA 7.36E-07
vg0405138328 sf0405133770 4 5138328 NA 3.72E-06
vg1215172315 sf1215169651 12 15172315 NA 3.75E-06
vg0820733365 sf0820730652 8 20733365 NA 4.15E-06