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 mr1156 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
vg0527924557 sf0527861914 5 27924557 1.77E-22 NA
vg1000281959 sf1000280959 10 281959 2.85E-22 NA
vg1013810037 sf1013738806 10 13810037 3.31E-22 NA
vg1217379600 sf1217373555 12 17379600 5.21E-22 NA
vg0919409649 sf0919409239 9 19409649 6.82E-22 NA
vg1215551723 sf1215549020 12 15551723 2.90E-21 NA
vg0229359655 sf0229353786 2 29359655 NA 3.72E-07
vg0229381690 sf0229375821 2 29381690 NA 1.54E-06
vg0515580789 sf0515523330 5 15580789 NA 3.87E-06
vg0221240541 sf0221234673 2 21240541 NA 3.93E-06
vg0500026327 sf0500026327 5 26327 NA 4.87E-06