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 mr1014 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
vg0133596348 sf0133595304 1 33596348 5.05E-102 1.94E-19
vg0133489903 sf0133488859 1 33489903 4.38E-101 1.60E-19
vg0130140335 sf0130139290 1 30140335 7.96E-84 NA
vg1014505092 sf1014433858 10 14505092 5.18E-78 4.50E-07
vg0130708537 sf0130707493 1 30708537 1.01E-77 6.36E-07
vg0214383856 sf0214377986 2 14383856 1.08E-76 NA
vg0221587239 sf0221581370 2 21587239 1.22E-76 NA
vg1208308635 sf1208306041 12 8308635 NA 2.09E-07
vg1015803765 sf1015732535 10 15803765 NA 5.35E-07
vg0133497043 sf0133495999 1 33497043 NA 7.24E-07
vg1020750336 sf1020678815 10 20750336 NA 1.51E-06
vg0203460456 sf0203460454 2 3460456 NA 2.52E-06
vg0706440810 sf0706439815 7 6440810 NA 4.50E-06
vg0433918347 sf0433733244 4 33918347 NA 4.77E-06
vg0801574405 sf0801573407 8 1574405 NA 9.79E-06