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 mr1152 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
vg0808437276 sf0808436280 8 8437276 1.21E-09 NA
vg1109493134 sf1109487711 11 9493134 2.15E-09 NA
vg0719333164 sf0719332171 7 19333164 4.42E-09 NA
vg1119761118 sf1119294806 11 19761118 6.96E-09 NA
vg0229918346 sf0229912477 2 29918346 2.78E-08 NA
vg1111258616 sf1111252933 11 11258616 2.33E-06 NA
vg1126435712 sf1125964125 11 26435712 8.03E-06 NA
vg1019396664 sf1019325219 10 19396664 8.61E-06 9.34E-07
vg1019396223 sf1019324778 10 19396223 NA 1.58E-06
vg0606957055 sf0606956056 6 6957055 NA 4.57E-06