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 mr1781 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
vg0900843177 sf0900842177 9 843177 3.11E-10 4.02E-06
vg0230813675 sf0230807806 2 30813675 5.04E-10 3.98E-06
vg0903779005 sf0903778005 9 3779005 2.12E-09 NA
vg1200182981 sf1200181981 12 182981 2.84E-09 7.95E-06
vg0130890135 sf0130889091 1 30890135 4.81E-09 NA
vg0225887862 sf0225881993 2 25887862 5.13E-09 5.53E-07
vg0131505293 sf0131504249 1 31505293 9.94E-09 4.80E-07
vg1106670681 sf1106666434 11 6670681 5.93E-07 3.50E-06