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 mr1931 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
vg0528326098 sf0528263453 5 28326098 2.78E-11 1.74E-06
vg0329226011 sf0329219063 3 29226011 1.52E-10 NA
vg0705219339 sf0705218340 7 5219339 1.73E-10 NA
vg1013888967 sf1013817735 10 13888967 2.19E-10 2.03E-06
vg0701643483 sf0701642484 7 1643483 2.62E-10 NA
vg0825757958 sf0825755244 8 25757958 3.41E-09 1.41E-06
vg0916332390 sf0916331389 9 16332390 NA 1.84E-06
vg1108800737 sf1108795347 11 8800737 NA 4.40E-06
vg1013894332 sf1013823100 10 13894332 NA 5.39E-06