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 mr1890 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
vg0216897057 sf0216891187 2 16897057 1.10E-08 1.67E-06
vg0500759356 sf0500759356 5 759356 3.47E-08 NA
vg0819513254 sf0819510541 8 19513254 4.40E-08 6.51E-06
vg0819320324 sf0819317611 8 19320324 1.13E-07 4.57E-06
vg0401024189 sf0401019741 4 1024189 1.82E-06 NA
vg0129154588 sf0129153543 1 29154588 2.62E-06 4.19E-06
vg0318243009 sf0318241791 3 18243009 9.37E-06 NA