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 mr1031 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
vg0130113615 sf0130112570 1 30113615 2.52E-11 NA
vg0123683628 sf0123682584 1 23683628 4.73E-09 NA
vg1111250824 sf1111245141 11 11250824 1.27E-06 NA
vg1117250681 sf1116784533 11 17250681 1.56E-06 3.74E-06
vg0910215512 sf0910214511 9 10215512 1.58E-06 NA
vg0621398092 sf0621397095 6 21398092 2.70E-06 2.12E-06
vg1215721018 sf1215718315 12 15721018 4.70E-06 NA
vg0324931493 sf0324929573 3 24931493 NA 5.18E-08