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 mr1521 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
vg0419217910 sf0419045948 4 19217910 7.78E-08 7.78E-08
vg0418931736 sf0418759781 4 18931736 2.82E-07 2.82E-07
vg1207186403 sf1207183793 12 7186403 3.22E-07 3.22E-07
vg1217950737 sf1217922172 12 17950737 9.98E-07 9.98E-07
vg0418802751 sf0418630796 4 18802751 1.26E-06 1.26E-06
vg0605633157 sf0605632158 6 5633157 1.40E-06 1.40E-06
vg0501597771 sf0501597755 5 1597771 2.00E-06 2.00E-06
vg0609140223 sf0609139224 6 9140223 2.07E-06 2.07E-06
vg0629124144 sf0629123146 6 29124144 3.70E-06 3.70E-06
vg0700065801 sf0700064801 7 65801 4.28E-06 4.28E-06
vg0115686548 sf0115685522 1 15686548 4.43E-06 4.43E-06