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 mr1987 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
vg0215052036 sf0215046166 2 15052036 5.93E-125 3.59E-10
vg0321280227 sf0321278737 3 21280227 1.88E-124 1.52E-09
vg0321287375 sf0321285885 3 21287375 3.82E-124 3.13E-10
vg0317721273 sf0317720055 3 17721273 9.61E-123 1.12E-08
vg0317750910 sf0317749692 3 17750910 2.07E-119 1.01E-08
vg0313856271 sf0313854988 3 13856271 6.66E-116 9.43E-07
vg0327028819 sf0327021872 3 27028819 1.80E-115 NA
vg0917797570 sf0917796569 9 17797570 1.87E-115 2.38E-07
vg0914766218 sf0914765217 9 14766218 2.25E-113 4.44E-06
vg0212524956 sf0212524952 2 12524956 4.87E-112 2.00E-06
vg0111834681 sf0111833655 1 11834681 1.51E-102 1.36E-06
vg1218760084 sf1218731519 12 18760084 NA 1.76E-07
vg0815172680 sf0815169966 8 15172680 NA 6.15E-07
vg0208620450 sf0208620449 2 8620450 NA 7.65E-07