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 mr1728 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
vg0918158744 sf0918157743 9 18158744 4.74E-32 1.84E-16
vg0918447666 sf0918446665 9 18447666 5.35E-28 3.82E-16
vg0916062006 sf0916061005 9 16062006 8.87E-17 NA
vg0917503526 sf0917502525 9 17503526 1.25E-13 3.62E-08
vg0919013922 sf0919012922 9 19013922 5.37E-12 1.61E-06
vg0915673890 sf0915672889 9 15673890 5.07E-09 NA
vg1203687735 sf1203686734 12 3687735 6.10E-09 NA
vg0513549972 sf0513492519 5 13549972 3.81E-07 NA
vg0607377849 sf0607376850 6 7377849 1.52E-06 4.13E-06
vg0607374248 sf0607373249 6 7374248 3.01E-06 2.95E-06
vg0332229065 sf0332221943 3 32229065 5.43E-06 NA
vg0910261090 sf0910260089 9 10261090 6.38E-06 4.68E-06
vg1005570850 sf1005587388 10 5570850 8.26E-06 NA
vg0332159587 sf0332152464 3 32159587 NA 2.67E-06
vg0920504790 sf0920504309 9 20504790 NA 2.73E-06