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 mr1089 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
vg0216744755 sf0216738885 2 16744755 2.17E-14 6.41E-06
vg0216547473 sf0216541603 2 16547473 6.12E-14 NA
vg0905825342 sf0905824342 9 5825342 7.96E-13 NA
vg0519667518 sf0519605002 5 19667518 5.46E-12 NA
vg0720232621 sf0720231628 7 20232621 8.42E-12 NA
vg0407230816 sf0407226086 4 7230816 2.20E-11 NA
vg0703938539 sf0703937540 7 3938539 NA 2.56E-06
vg0625171406 sf0625170409 6 25171406 NA 2.77E-06