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 mr1289 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
vg0103416626 sf0103415626 1 3416626 6.13E-07 1.01E-06
vg1217937627 sf1217909061 12 17937627 1.57E-06 4.67E-06
vg0119275798 sf0119274753 1 19275798 8.65E-06 NA
vg0622302379 sf0622301382 6 22302379 NA 1.42E-06
vg1210846837 sf1210844203 12 10846837 NA 2.84E-06
vg0623599305 sf0623598308 6 23599305 NA 9.30E-06