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 mr1916 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
vg0801654175 sf0801653177 8 1654175 2.95E-11 3.89E-06
vg0102687164 sf0102686164 1 2687164 9.00E-11 1.68E-07
vg0507245949 sf0507245891 5 7245949 6.24E-10 NA
vg0904379272 sf0904378272 9 4379272 8.43E-10 NA
vg0125687545 sf0125686501 1 25687545 8.72E-10 NA
vg0106807246 sf0106806246 1 6807246 2.88E-09 9.19E-06