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 mr1603 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
vg0216763017 sf0216757147 2 16763017 5.10E-14 5.31E-10
vg1004292753 sf1004309291 10 4292753 2.50E-12 4.72E-06
vg1214834416 sf1214831757 12 14834416 1.27E-10 NA
vg0218324782 sf0218318913 2 18324782 5.15E-09 4.81E-07
vg1214952929 sf1214950271 12 14952929 6.43E-09 NA
vg0217031670 sf0217025800 2 17031670 6.61E-09 8.20E-07
vg0528784412 sf0528721767 5 28784412 3.52E-07 3.34E-06
vg0908091687 sf0908090687 9 8091687 1.42E-06 NA
vg0218467788 sf0218461919 2 18467788 5.76E-06 3.47E-06
vg0516132563 sf0516075047 5 16132563 8.41E-06 1.15E-06
Unknow sf0433825480 Unknow Unknow NA 1.51E-06
vg0921835488 sf0921835007 9 21835488 NA 3.90E-06