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 mr1627 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
vg0512704119 sf0512647041 5 12704119 7.19E-13 6.15E-07
vg0117236820 sf0117235774 1 17236820 1.36E-12 4.23E-07
vg0122048209 sf0122047164 1 22048209 1.99E-11 9.56E-07
vg0509836819 sf0509836748 5 9836819 2.38E-11 NA
vg0414404728 sf0414395441 4 14404728 2.87E-11 NA
vg0508461245 sf0508461173 5 8461245 6.32E-11 NA
vg0122145785 sf0122144740 1 22145785 2.20E-10 2.77E-08
vg0910500550 sf0910499549 9 10500550 1.98E-07 3.57E-06
vg1224316333 sf1224282786 12 24316333 NA 2.63E-06
vg1224314963 sf1224281416 12 24314963 NA 2.95E-06
vg0334406362 sf0334399232 3 34406362 NA 3.00E-06
vg1103961340 sf1103957242 11 3961340 NA 8.71E-06