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 mr1033 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
vg0613453861 sf0613452862 6 13453861 1.12E-20 4.51E-15
vg0617852624 sf0617851627 6 17852624 2.44E-20 9.41E-15
vg0619176470 sf0619175473 6 19176470 NA 7.36E-07
vg0613194984 sf0613193985 6 13194984 NA 1.90E-06
vg0621021467 sf0621020470 6 21021467 NA 3.04E-06