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 mr1264 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
vg0719039736 sf0719038743 7 19039736 2.56E-09 2.56E-09
vg0719156501 sf0719155508 7 19156501 2.11E-08 2.11E-08
vg0719125702 sf0719124709 7 19125702 2.88E-08 2.88E-08
vg0414596511 sf0414587225 4 14596511 7.31E-07 7.31E-07
vg1100663631 sf1100662634 11 663631 9.21E-07 9.21E-07
vg0329561125 sf0329554165 3 29561125 1.25E-06 1.25E-06
vg0126418162 sf0126417118 1 26418162 2.40E-06 2.40E-06
vg0422276479 sf0422091361 4 22276479 2.82E-06 2.82E-06
vg0208043154 sf0208043153 2 8043154 3.13E-06 3.13E-06
vg0723875740 sf0723874746 7 23875740 3.28E-06 3.28E-06
vg0123250426 sf0123249382 1 23250426 3.43E-06 3.43E-06
vg1125341795 sf1124875635 11 25341795 4.02E-06 4.02E-06
vg0819291197 sf0819288484 8 19291197 4.80E-06 4.80E-06
vg0209814019 sf0209814017 2 9814019 4.84E-06 4.84E-06