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 mr1036 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
vg0401231092 sf0401226642 4 1231092 9.56E-08 NA
vg0208262087 sf0208262086 2 8262087 8.47E-06 NA
vg0804315505 sf0804314508 8 4315505 NA 2.11E-07
vg0804312174 sf0804311177 8 4312174 NA 2.47E-07
vg0804315269 sf0804314272 8 4315269 NA 4.34E-07
vg0217956643 sf0217950774 2 17956643 NA 2.00E-06