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 mr1522 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
vg0139046810 sf0139045767 1 39046810 2.53E-08 5.76E-06
vg0418071347 sf0417899388 4 18071347 2.13E-06 NA
vg0129767620 sf0129766575 1 29767620 NA 9.11E-07
vg0809841368 sf0809840372 8 9841368 NA 1.32E-06
vg0129794216 sf0129793171 1 29794216 NA 4.82E-06