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 mr1681 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
vg1219760769 sf1219732239 12 19760769 3.85E-13 1.06E-08
vg1219779242 sf1219750712 12 19779242 3.95E-13 8.99E-09
vg0130297483 sf0130296438 1 30297483 1.00E-11 1.81E-06
vg0618527729 sf0618526732 6 18527729 4.82E-11 4.11E-06
vg0820029176 sf0820026463 8 20029176 5.00E-11 2.25E-06
vg0433322485 sf0433137375 4 33322485 6.10E-11 NA
vg0130318336 sf0130317292 1 30318336 7.05E-11 1.73E-07
vg0919082937 sf0919082526 9 19082937 NA 1.28E-06
vg0618214950 sf0618213953 6 18214950 NA 1.45E-06
vg1214134657 sf1214131997 12 14134657 NA 3.44E-06