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 mr1003 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
vg0921457375 sf0921456894 9 21457375 1.55E-09 7.06E-07
vg0921543752 sf0921543271 9 21543752 3.32E-09 8.36E-09
vg0134815001 sf0134813958 1 34815001 3.52E-09 NA
vg0328947114 sf0328940166 3 28947114 4.65E-09 8.03E-06
vg0328947425 sf0328940477 3 28947425 4.85E-09 5.10E-07
vg0139123162 sf0139122119 1 39123162 3.22E-08 NA
vg0626417085 sf0626416088 6 26417085 3.46E-08 NA
vg0328828618 sf0328821672 3 28828618 1.74E-07 NA
vg0133599398 sf0133598354 1 33599398 3.34E-07 1.02E-06
vg0215099729 sf0215093859 2 15099729 1.30E-06 2.38E-06