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 mr1445 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
vg1117583959 sf1117117816 11 17583959 1.88E-10 NA
vg0922565216 sf0922564735 9 22565216 2.88E-09 NA
vg0105158575 sf0105157575 1 5158575 4.38E-09 3.87E-06
vg0500210699 sf0500210699 5 210699 4.64E-09 9.96E-06
vg0105160384 sf0105159384 1 5160384 5.41E-09 5.19E-06
vg0332501464 sf0332494337 3 32501464 7.90E-09 NA
vg0500282600 sf0500282600 5 282600 5.26E-08 2.54E-06
vg0224207984 sf0224202115 2 24207984 1.77E-07 5.07E-06
vg0602873031 sf0602872032 6 2873031 2.61E-07 NA
vg0907441318 sf0907440318 9 7441318 2.89E-06 NA