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 mr1263 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
vg0141835378 sf0141834335 1 41835378 4.40E-09 NA
vg0141835922 sf0141834879 1 41835922 7.78E-09 NA
vg0907578649 sf0907577649 9 7578649 1.19E-06 5.71E-08
vg0141761592 sf0141760549 1 41761592 4.76E-06 4.31E-06
vg0334445299 sf0334438169 3 34445299 NA 3.61E-07