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 mr1311 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
vg0332498725 sf0332491598 3 32498725 5.20E-08 3.72E-06
vg0420836195 sf0420664238 4 20836195 7.30E-08 3.76E-06
vg0434012329 sf0433827220 4 34012329 7.42E-08 2.49E-06
vg0420830218 sf0420658261 4 20830218 3.10E-07 1.08E-06
vg0402100710 sf0402096304 4 2100710 7.91E-07 1.98E-06
vg0406886096 sf0406881355 4 6886096 3.01E-06 2.10E-07
vg0408141966 sf0408137240 4 8141966 6.49E-06 1.46E-06