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 mr1232 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
vg0123690615 sf0123689571 1 23690615 2.13E-11 NA
vg0918496669 sf0918495668 9 18496669 4.54E-11 4.82E-06
vg0106581088 sf0106580088 1 6581088 1.97E-10 NA
vg0919909414 sf0919908933 9 19909414 5.98E-10 NA
vg0821932616 sf0821929903 8 21932616 7.74E-10 NA
vg0335349500 sf0335342369 3 35349500 1.92E-08 4.77E-06
vg0130351635 sf0130350591 1 30351635 1.03E-06 NA
vg0119413705 sf0119412660 1 19413705 1.08E-06 NA
vg1202109317 sf1202108315 12 2109317 3.59E-06 NA
vg0431655631 sf0431470524 4 31655631 NA 3.36E-06