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 mr1393 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
vg0507173622 sf0507173564 5 7173622 4.79E-07 4.79E-07
vg0235128192 sf0235122323 2 35128192 5.53E-07 5.53E-07
vg0406862378 sf0406857823 4 6862378 1.52E-06 1.52E-06
vg0512875775 sf0512818697 5 12875775 2.94E-06 2.94E-06
vg0513542683 sf0513485230 5 13542683 3.73E-06 3.73E-06