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 mr1222 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
vg0222739655 sf0222733786 2 22739655 1.27E-20 1.74E-18
vg0224274080 sf0224268211 2 24274080 8.38E-09 7.40E-07
vg0222634177 sf0222628308 2 22634177 9.78E-08 3.23E-06
vg0222684953 sf0222679084 2 22684953 2.17E-07 1.35E-06
vg0610462510 sf0610461511 6 10462510 1.20E-06 3.51E-06
vg0216799875 sf0216794005 2 16799875 4.88E-06 1.80E-07
vg0223077654 sf0223071785 2 23077654 6.67E-06 1.78E-06