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 mr1860 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 1.86E-21 8.04E-14
vg0916209370 sf0916208369 9 16209370 7.95E-14 1.41E-06
vg0324608474 sf0324606553 3 24608474 3.51E-10 2.38E-06
vg0919013922 sf0919012922 9 19013922 3.58E-10 NA
vg0915673890 sf0915672889 9 15673890 2.62E-09 NA
vg0619422571 sf0619421574 6 19422571 2.25E-08 4.84E-07
vg0333676840 sf0333669710 3 33676840 2.40E-07 2.07E-06
vg0820029453 sf0820026740 8 20029453 5.11E-07 9.54E-07
vg0332229065 sf0332221943 3 32229065 5.19E-07 3.75E-06
vg0618947595 sf0618946598 6 18947595 7.11E-07 2.61E-06
vg0332124562 sf0332117439 3 32124562 5.12E-06 NA
vg0910198203 sf0910197202 9 10198203 NA 3.85E-07
vg0816191471 sf0816188757 8 16191471 NA 9.26E-07
vg0219817547 sf0219811679 2 19817547 NA 1.42E-06
vg0404393271 sf0404388875 4 4393271 NA 3.80E-06