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 mr1336 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
vg0300375981 sf0300374979 3 375981 5.23E-10 NA
vg0909341912 sf0909340911 9 9341912 4.38E-09 NA
vg0142781339 sf0142780295 1 42781339 4.80E-09 NA
vg0519281720 sf0519219204 5 19281720 5.40E-09 NA
vg0411116007 sf0411106708 4 11116007 6.81E-09 NA
vg1214761316 sf1214758657 12 14761316 3.68E-07 NA
vg1011837512 sf1011766327 10 11837512 3.82E-07 3.21E-06
vg0523191092 sf0523128533 5 23191092 5.05E-07 NA
vg0519821208 sf0519758684 5 19821208 1.49E-06 NA
vg0800338957 sf0800337957 8 338957 2.32E-06 NA