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 mr1657 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
vg0220287168 sf0220281300 2 20287168 1.19E-07 1.19E-07
vg0220283766 sf0220277898 2 20283766 1.47E-07 1.47E-07
vg0416930919 sf0416758961 4 16930919 3.12E-07 3.12E-07
vg0321576473 sf0321574983 3 21576473 8.60E-07 8.60E-07
vg1125299435 sf1124833275 11 25299435 1.82E-06 1.82E-06
vg0203468898 sf0203468896 2 3468898 2.32E-06 2.32E-06
vg1204515146 sf1204514134 12 4515146 2.68E-06 2.68E-06
vg0321577849 sf0321576359 3 21577849 2.78E-06 2.78E-06
vg0909184912 sf0909183911 9 9184912 4.93E-06 4.93E-06