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 mr1583 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
vg1122937279 sf1122471150 11 22937279 1.45E-09 5.11E-07
vg0502976477 sf0502976453 5 2976477 1.70E-09 7.23E-07
vg0506207863 sf0506207802 5 6207863 2.79E-09 4.89E-07
vg1209813012 sf1209810422 12 9813012 3.32E-09 9.13E-07
vg0116398776 sf0116397750 1 16398776 3.75E-09 NA