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 mr1393 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
vg0422578975 sf0422393858 4 22578975 1.30E-09 1.78E-06
vg0700312059 sf0700311059 7 312059 1.96E-08 NA
vg0329241236 sf0329234288 3 29241236 5.20E-08 NA
vg0909460279 sf0909459278 9 9460279 5.77E-08 NA
vg0315312443 sf0315311090 3 15312443 6.25E-08 NA