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 mr1837 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
vg0526515824 sf0526453188 5 26515824 1.70E-10 NA
vg0728875743 sf0728874751 7 28875743 1.72E-10 NA
vg0317321849 sf0317320659 3 17321849 2.54E-10 NA
vg0118270990 sf0118269944 1 18270990 3.11E-10 NA
vg0431615949 sf0431430844 4 31615949 4.89E-10 NA
vg0431515534 sf0431330433 4 31515534 1.94E-09 8.82E-07
vg1115981616 sf1115516488 11 15981616 1.15E-07 NA
vg1125281259 sf1124815099 11 25281259 2.02E-07 NA