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 mr1291 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
vg0200469050 sf0200469050 2 469050 1.80E-08 NA
vg0101656901 sf0101655901 1 1656901 3.92E-08 NA
vg0618212179 sf0618211182 6 18212179 4.15E-08 3.42E-06
vg0103132262 sf0103131262 1 3132262 4.35E-08 NA
vg0619397284 sf0619396287 6 19397284 4.38E-08 1.53E-06
vg0316213365 sf0316212013 3 16213365 6.58E-08 NA
vg0910045544 sf0910044543 9 10045544 NA 3.49E-06
vg0232159658 sf0232153789 2 32159658 NA 3.89E-06
vg0200349177 sf0200349177 2 349177 NA 6.24E-06