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 mr1567 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
vg0525126223 sf0525063638 5 25126223 3.86E-08 NA
vg1012856484 sf1012785299 10 12856484 5.39E-08 NA
vg0806440451 sf0806439456 8 6440451 5.70E-08 6.96E-06
vg1117195800 sf1116729652 11 17195800 6.80E-08 NA
vg0807410855 sf0807409860 8 7410855 7.16E-08 2.06E-06
vg0805595734 sf0805594737 8 5595734 1.03E-07 4.84E-06
vg0203000556 sf0203000554 2 3000556 9.57E-07 NA
vg1104963383 sf1104959194 11 4963383 2.46E-06 NA
vg0118071019 sf0118069973 1 18071019 3.73E-06 NA
vg1122207231 sf1121741102 11 22207231 8.62E-06 NA
vg0209213128 sf0209213126 2 9213128 9.52E-06 NA