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 mr1702 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
vg0919961970 sf0919961489 9 19961970 6.87E-07 NA
vg1218662517 sf1218633952 12 18662517 7.51E-07 2.86E-06
vg1004572532 sf1004589070 10 4572532 NA 5.25E-07
vg0202324483 sf0202324481 2 2324483 NA 2.74E-06
vg0607375453 sf0607374454 6 7375453 NA 3.13E-06
vg0304944718 sf0304943720 3 4944718 NA 3.35E-06
vg0903523933 sf0903522933 9 3523933 NA 3.85E-06