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 mr1448 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
vg0208157049 sf0208157048 2 8157049 3.33E-08 1.70E-06
vg0113970354 sf0113969328 1 13970354 1.16E-07 3.14E-06
vg0601262655 sf0601261656 6 1262655 3.15E-07 1.80E-06
vg1200180797 sf1200179797 12 180797 4.82E-07 7.89E-06
vg0428960374 sf0428775232 4 28960374 3.00E-06 6.15E-06