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 mr1507 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
vg1117584893 sf1117118750 11 17584893 6.97E-07 6.97E-07
vg0328103960 sf0328097014 3 28103960 7.71E-07 7.71E-07
vg0328939602 sf0328932654 3 28939602 1.40E-06 1.40E-06
vg1127125428 sf1126653815 11 27125428 1.56E-06 1.56E-06
vg0432023793 sf0431838686 4 32023793 2.01E-06 2.01E-06
vg0626887934 sf0626886937 6 26887934 2.32E-06 2.32E-06
vg0208850397 sf0208850395 2 8850397 3.11E-06 3.11E-06
vg0916455234 sf0916454233 9 16455234 4.43E-06 4.43E-06
vg0327981236 sf0327974290 3 27981236 4.55E-06 4.55E-06
vg0207461142 sf0207461142 2 7461142 4.93E-06 4.93E-06