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 mr1665 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
vg0315358592 sf0315357239 3 15358592 5.09E-11 NA
vg0312560454 sf0312559172 3 12560454 1.11E-10 NA
vg0818230180 sf0818227467 8 18230180 8.30E-10 NA
vg0332499847 sf0332492720 3 32499847 1.69E-09 NA
vg0406987146 sf0406982417 4 6987146 2.43E-09 NA
vg0323778716 sf0323776890 3 23778716 3.11E-07 1.01E-06
vg1128647951 sf1128124730 11 28647951 7.79E-07 1.80E-06
vg0909448931 sf0909447930 9 9448931 1.24E-06 NA
vg0922414567 sf0922414086 9 22414567 1.47E-06 NA
vg0407140848 sf0407136118 4 7140848 NA 8.78E-07