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 mr1830 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
vg0411404313 sf0411395016 4 11404313 1.23E-16 4.64E-08
vg0413988245 sf0413978960 4 13988245 2.89E-16 NA
vg0408482568 sf0408477841 4 8482568 1.77E-15 1.49E-06
vg0407126253 sf0407121523 4 7126253 7.55E-14 5.75E-07
vg0406833198 sf0406828643 4 6833198 2.90E-12 NA
vg0614459942 sf0614458943 6 14459942 7.58E-12 NA
vg0821751104 sf0821748391 8 21751104 4.50E-10 NA
vg0920468505 sf0920468024 9 20468505 5.83E-08 NA
vg0724004854 sf0724003860 7 24004854 2.88E-07 NA
vg0826935517 sf0826932803 8 26935517 3.54E-07 NA
vg0913502351 sf0913501350 9 13502351 NA 1.86E-06