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 mr1063 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
vg0612914787 sf0612913788 6 12914787 1.25E-15 NA
vg0617359224 sf0617358227 6 17359224 1.30E-15 NA
vg0805574630 sf0805573633 8 5574630 1.04E-13 NA
vg0805570467 sf0805569470 8 5570467 2.98E-13 NA
vg0335449717 sf0335442586 3 35449717 1.13E-12 NA
vg0809373030 sf0809372034 8 9373030 1.25E-12 NA
vg0222739831 sf0222733962 2 22739831 1.72E-09 1.20E-13
vg0139856893 sf0139855850 1 39856893 4.61E-08 NA
vg0223668140 sf0223662271 2 23668140 1.40E-07 7.43E-07
vg0220610874 sf0220605006 2 20610874 8.57E-07 NA
vg0223708173 sf0223702304 2 23708173 8.61E-07 2.88E-06
vg1113860205 sf1113396526 11 13860205 NA 2.23E-06
vg0411135218 sf0411125919 4 11135218 NA 2.64E-06
vg0608528871 sf0608527872 6 8528871 NA 2.68E-06
vg0301547360 sf0301546356 3 1547360 NA 8.07E-06