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 mr1317 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
vg0217073423 sf0217067553 2 17073423 1.38E-07 1.38E-07
vg0202784765 sf0202784763 2 2784765 7.05E-07 7.05E-07
vg1221738881 sf1221705428 12 21738881 7.84E-07 7.84E-07
vg0103188464 sf0103187464 1 3188464 1.63E-06 1.63E-06
vg1123928854 sf1123462724 11 23928854 3.26E-06 3.26E-06
vg0203435445 sf0203435443 2 3435445 3.34E-06 3.34E-06
vg0619610063 sf0619609066 6 19610063 3.49E-06 3.49E-06
vg1107849096 sf1107844841 11 7849096 3.72E-06 3.72E-06
vg0210369537 sf0210369535 2 10369537 4.71E-06 4.71E-06