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 mr1854 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
vg0726964336 sf0726963342 7 26964336 5.94E-08 NA
vg0224007952 sf0224002083 2 24007952 6.88E-07 2.71E-06
vg0435137768 sf0434952650 4 35137768 2.97E-06 6.99E-06
vg1016429449 sf1016358223 10 16429449 5.47E-06 7.78E-07
vg1115066964 sf1114603278 11 15066964 NA 9.61E-06