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 mr1002 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
vg1210111063 sf1210108474 12 10111063 1.42E-09 NA
vg1207825767 sf1207823173 12 7825767 2.09E-09 NA
vg0617102404 sf0617101407 6 17102404 4.71E-09 1.15E-07
vg0520132230 sf0520069703 5 20132230 5.09E-09 NA
vg0431440977 sf0431255875 4 31440977 5.22E-09 NA
vg1005490148 sf1005506685 10 5490148 4.24E-08 7.09E-06
vg0701855566 sf0701854567 7 1855566 1.36E-07 3.58E-06
vg0709172569 sf0709171575 7 9172569 1.58E-07 7.54E-07
vg0212939891 sf0212939887 2 12939891 5.19E-07 4.98E-06
vg0208783505 sf0208783503 2 8783505 2.56E-06 1.16E-06
vg0919842296 sf0919841815 9 19842296 9.73E-06 NA