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 mr1510 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
vg0420194426 sf0420022466 4 20194426 1.13E-09 NA
vg0721444548 sf0721443555 7 21444548 1.19E-09 NA
vg0417919001 sf0417747042 4 17919001 6.64E-09 NA
vg0709616672 sf0709615678 7 9616672 7.63E-09 NA
vg0607375701 sf0607374702 6 7375701 8.78E-09 NA
vg0124101489 sf0124100445 1 24101489 6.74E-08 4.82E-06
vg0412274018 sf0412264733 4 12274018 2.37E-07 NA
vg0313932293 sf0313931010 3 13932293 6.84E-07 NA