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 mr1888 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
vg1207710323 sf1207707727 12 7710323 4.77E-09 NA
vg0715027149 sf0715026156 7 15027149 1.06E-08 NA
vg0307861794 sf0307860732 3 7861794 5.58E-08 NA
vg0226057933 sf0226052064 2 26057933 1.93E-07 1.64E-06
vg0726566560 sf0726565566 7 26566560 1.13E-06 NA
vg0708973974 sf0708972980 7 8973974 NA 1.54E-06