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 mr1784 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
vg1018574905 sf1018503462 10 18574905 7.98E-53 1.19E-11
vg0516106056 sf0516048540 5 16106056 4.92E-45 NA
vg1016045545 sf1015974317 10 16045545 2.62E-41 NA
vg0815931155 sf0815928441 8 15931155 8.84E-41 NA
vg1216410025 sf1216407318 12 16410025 5.46E-40 NA
vg1018466898 sf1018395455 10 18466898 NA 3.16E-07
vg1205550390 sf1205549376 12 5550390 NA 2.38E-06
vg0800063298 sf0800062298 8 63298 NA 4.32E-06