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 mr1759 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
vg0133294457 sf0133293413 1 33294457 2.52E-10 NA
vg0123696162 sf0123695118 1 23696162 3.93E-10 NA
vg0105761092 sf0105760092 1 5761092 6.48E-10 NA
vg0819439794 sf0819437081 8 19439794 4.41E-09 1.18E-06
vg0131567146 sf0131566102 1 31567146 6.27E-09 NA
vg0805992743 sf0805991746 8 5992743 3.15E-08 2.01E-07
vg0409570147 sf0409560845 4 9570147 1.10E-06 NA
vg1125669886 sf1125203725 11 25669886 3.00E-06 NA
vg0719335637 sf0719334644 7 19335637 3.34E-06 NA
vg1214134657 sf1214131997 12 14134657 3.44E-06 3.26E-06
vg1207840460 sf1207837866 12 7840460 NA 8.49E-07