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 mr1680 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
vg0506124564 sf0506124503 5 6124564 1.08E-07 1.08E-07
vg0224249203 sf0224243334 2 24249203 1.34E-07 1.34E-07
vg0900901867 sf0900900867 9 901867 4.35E-07 4.35E-07
vg0904311174 sf0904310174 9 4311174 5.19E-07 5.19E-07
vg0226083118 sf0226077249 2 26083118 1.04E-06 1.04E-06
vg0224477732 sf0224471863 2 24477732 3.40E-06 3.40E-06