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 mr1678 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
vg0200743118 sf0200743118 2 743118 1.09E-08 NA
vg0506747780 sf0506747722 5 6747780 3.57E-08 4.40E-06
vg0506746775 sf0506746717 5 6746775 5.08E-08 1.88E-06
vg0100936862 sf0100935862 1 936862 5.38E-08 NA
vg0200805927 sf0200805927 2 805927 5.72E-08 NA
vg0509902421 sf0509902350 5 9902421 1.09E-07 4.55E-06
vg0919408593 sf0919408183 9 19408593 1.93E-07 3.22E-06
vg0200806828 sf0200806828 2 806828 6.78E-07 NA
vg0821122833 sf0821120120 8 21122833 9.70E-07 2.85E-06
vg0330038160 sf0330031199 3 30038160 2.16E-06 NA