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 mr1766 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
vg0123461399 sf0123460355 1 23461399 8.73E-08 8.75E-08
vg1020531763 sf1020460242 10 20531763 2.27E-07 2.27E-07
vg1020531779 sf1020460258 10 20531779 3.26E-07 3.27E-07
vg0220342715 sf0220336847 2 20342715 9.70E-07 9.72E-07
vg0805992743 sf0805991746 8 5992743 1.57E-06 1.58E-06
vg0801697883 sf0801696886 8 1697883 1.76E-06 1.76E-06
vg0717735595 sf0717734602 7 17735595 2.17E-06 2.18E-06
vg0102107447 sf0102106447 1 2107447 2.55E-06 2.55E-06
vg0715011230 sf0715010237 7 15011230 2.97E-06 2.97E-06
vg0421121684 sf0420949736 4 21121684 3.14E-06 3.14E-06
vg1118023722 sf1117557580 11 18023722 3.14E-06 3.15E-06
vg0105514748 sf0105513748 1 5514748 3.49E-06 3.50E-06
vg1112652709 sf1112189030 11 12652709 4.11E-06 4.12E-06
vg0715008269 sf0715007276 7 15008269 4.87E-06 4.86E-06