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 mr1873 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
vg0818674921 sf0818672208 8 18674921 1.15E-08 1.15E-08
vg0819016766 sf0819014053 8 19016766 1.33E-08 1.33E-08
vg0603303699 sf0603302700 6 3303699 6.53E-07 6.53E-07
vg0335572253 sf0335565122 3 35572253 1.27E-06 1.28E-06
vg0801772486 sf0801771489 8 1772486 2.59E-06 2.59E-06
vg0900852915 sf0900851915 9 852915 3.32E-06 3.33E-06
vg0715468281 sf0715467288 7 15468281 4.88E-06 4.89E-06