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 mr1246 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
vg0719011406 sf0719010413 7 19011406 2.45E-41 5.86E-30
vg0717192350 sf0717191357 7 17192350 5.41E-14 2.78E-08
vg1201654412 sf1201653412 12 1654412 2.06E-13 4.35E-06
vg0918899144 sf0918898144 9 18899144 9.36E-13 NA
vg0718885795 sf0718884802 7 18885795 1.22E-12 4.62E-11
vg1201345907 sf1201344907 12 1345907 3.98E-12 2.60E-06
vg0707515285 sf0707514290 7 7515285 5.70E-12 3.72E-08
vg0305031973 sf0305030975 3 5031973 2.17E-11 2.34E-08
vg0918912349 sf0918911349 9 18912349 2.60E-11 NA
vg0305009028 sf0305008030 3 5009028 6.39E-08 1.47E-08
vg0315179733 sf0315178380 3 15179733 1.28E-07 1.54E-06
vg0719484075 sf0719483082 7 19484075 1.09E-06 1.25E-06
vg0719209824 sf0719208831 7 19209824 2.81E-06 1.52E-07
vg0221873638 sf0221867769 2 21873638 3.53E-06 NA
vg0139656695 sf0139655652 1 39656695 3.60E-06 1.63E-07
vg0718985745 sf0718984752 7 18985745 NA 2.02E-11
vg0711114579 sf0711113585 7 11114579 NA 1.36E-06
vg1124078197 sf1123612067 11 24078197 NA 3.22E-06
vg0410037810 sf0410028507 4 10037810 NA 3.23E-06
vg0421119918 sf0420947970 4 21119918 NA 3.24E-06
vg1014690218 sf1014618984 10 14690218 NA 4.90E-06