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 mr1236 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
vg0106722456 sf0106721456 1 6722456 6.82E-13 4.59E-08
vg1214243584 sf1214240924 12 14243584 1.74E-09 NA
vg0914018847 sf0914017846 9 14018847 1.77E-09 NA
vg1108715769 sf1108710379 11 8715769 8.01E-09 NA
vg1001593604 sf1001592581 10 1593604 1.26E-08 NA
vg0712394149 sf0712393156 7 12394149 9.73E-07 NA
vg0208432932 sf0208432931 2 8432932 1.02E-06 7.75E-06
vg1216321299 sf1216318595 12 16321299 NA 1.36E-06