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 mr1842 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
vg0621137518 sf0621136521 6 21137518 4.80E-08 4.80E-08
vg0400999452 sf0400995004 4 999452 3.38E-07 3.38E-07
vg1122003288 sf1121537159 11 22003288 7.39E-07 7.39E-07
vg0200600738 sf0200600738 2 600738 7.48E-07 7.48E-07
vg0400871651 sf0400870651 4 871651 1.44E-06 1.44E-06
vg0725312603 sf0725311609 7 25312603 1.49E-06 1.49E-06
vg0714477799 sf0714476806 7 14477799 1.72E-06 1.72E-06
vg0217197904 sf0217192034 2 17197904 2.20E-06 2.20E-06
vg0808091194 sf0808090198 8 8091194 4.09E-06 4.09E-06
vg0504188501 sf0504188478 5 4188501 4.49E-06 4.48E-06