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 mr1046 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
vg1218168002 sf1218139438 12 18168002 1.49E-06 1.49E-06
vg0826159919 sf0826157205 8 26159919 1.73E-06 1.74E-06
vg1117431373 sf1116965228 11 17431373 2.50E-06 2.50E-06
vg1017098057 sf1017026829 10 17098057 2.59E-06 2.59E-06
vg0620348476 sf0620347479 6 20348476 3.48E-06 3.48E-06
vg0601223619 sf0601222620 6 1223619 4.34E-06 4.34E-06
vg1122446629 sf1121980500 11 22446629 4.83E-06 4.83E-06
vg0327981236 sf0327974290 3 27981236 6.85E-06 6.85E-06