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 mr1358 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
vg0224822504 sf0224816635 2 24822504 5.78E-09 5.79E-09
vg0629378360 sf0629377362 6 29378360 3.89E-07 3.89E-07
vg1122446629 sf1121980500 11 22446629 2.20E-06 2.20E-06
vg0812794506 sf0812792331 8 12794506 2.72E-06 2.72E-06
vg0136576949 sf0136575906 1 36576949 3.89E-06 3.89E-06