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 mr1358 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
vg1214568067 sf1214565408 12 14568067 6.01E-09 1.53E-08
vg0306324536 sf0306323536 3 6324536 7.03E-09 NA
vg1214552269 sf1214549610 12 14552269 7.23E-09 1.47E-08
vg0726964336 sf0726963342 7 26964336 8.32E-09 NA
vg0129486709 sf0129485664 1 29486709 1.30E-08 NA
vg0129469514 sf0129468469 1 29469514 1.42E-08 3.23E-06
vg0125510468 sf0125509424 1 25510468 3.34E-08 NA
vg0630306971 sf0630305973 6 30306971 4.72E-08 6.11E-06
vg0327968455 sf0327961509 3 27968455 3.82E-06 4.82E-06
vg0804208300 sf0804207303 8 4208300 7.72E-06 NA