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 mr1991 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
vg0207214824 sf0207214824 2 7214824 7.30E-10 2.00E-08
vg0906785691 sf0906784691 9 6785691 1.02E-08 1.47E-07
vg1003063551 sf1003062528 10 3063551 5.20E-08 1.19E-06
vg0115241228 sf0115240202 1 15241228 7.56E-08 1.22E-06
vg0324021677 sf0324019850 3 24021677 1.65E-07 3.94E-06
vg0112338981 sf0112337955 1 12338981 2.07E-07 4.19E-06
vg0500883408 sf0500883390 5 883408 2.58E-07 4.72E-06
vg1121909998 sf1121443869 11 21909998 5.16E-07 3.97E-06