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 mr1712 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
vg0820747994 sf0820745281 8 20747994 2.25E-07 2.48E-07
vg0820477021 sf0820474308 8 20477021 5.83E-07 1.13E-06
vg1218040492 sf1218011928 12 18040492 1.75E-06 1.25E-06
vg0602991597 sf0602990598 6 2991597 4.63E-06 3.99E-06
vg0913504506 sf0913503505 9 13504506 5.84E-06 3.01E-06
vg0116191559 sf0116190533 1 16191559 6.19E-06 NA
vg0122960572 sf0122959528 1 22960572 NA 1.47E-06
vg0514934174 sf0514876717 5 14934174 NA 7.01E-06