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 mr1298 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
vg0433403124 sf0433218013 4 33403124 2.63E-27 1.56E-07
vg0800325236 sf0800324236 8 325236 4.26E-27 NA
vg0433421279 sf0433236168 4 33421279 1.88E-25 4.32E-06
vg1209153454 sf1209150863 12 9153454 3.56E-25 NA
vg0710733941 sf0710732947 7 10733941 8.82E-25 NA
vg0627047035 sf0627046038 6 27047035 1.18E-24 NA
vg1214656787 sf1214654127 12 14656787 2.00E-23 3.75E-06
vg0820974361 sf0820971648 8 20974361 2.88E-22 NA
vg0800292156 sf0800291156 8 292156 NA 1.46E-08
vg0800344884 sf0800343884 8 344884 NA 8.15E-08
vg1214134657 sf1214131997 12 14134657 NA 5.89E-07
vg0906631032 sf0906630032 9 6631032 NA 7.87E-07
vg0223147995 sf0223142126 2 23147995 NA 1.36E-06
vg0700285828 sf0700284828 7 285828 NA 2.86E-06