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 mr1548 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
vg1000850801 sf1000849777 10 850801 4.78E-11 1.50E-06
vg0501178896 sf0501178880 5 1178896 1.89E-09 NA
vg0314437380 sf0314436068 3 14437380 2.43E-09 NA
vg0512839822 sf0512782744 5 12839822 5.57E-09 NA
vg0122048209 sf0122047164 1 22048209 1.12E-08 NA