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 mr1699 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
vg0331120461 sf0331109198 3 31120461 3.04E-14 1.36E-10
vg0824847711 sf0824844997 8 24847711 7.13E-10 3.76E-07
vg1126645421 sf1126173836 11 26645421 1.07E-08 7.47E-08
vg0107145470 sf0107144470 1 7145470 1.24E-08 5.98E-07
vg0107072026 sf0107071026 1 7072026 2.95E-08 4.76E-07
vg0821385042 sf0821382329 8 21385042 3.91E-08 NA
vg0823144076 sf0823141363 8 23144076 6.53E-08 2.39E-07
vg0234213524 sf0234207655 2 34213524 1.73E-06 1.90E-08