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 mr1404 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
vg0719090536 sf0719089543 7 19090536 3.08E-62 9.47E-25
vg0719302457 sf0719301464 7 19302457 1.30E-58 1.06E-25
vg0719006168 sf0719005175 7 19006168 3.19E-53 1.89E-16
vg0719062929 sf0719061936 7 19062929 8.44E-47 6.70E-17
vg0917782314 sf0917781313 9 17782314 9.62E-41 NA
vg1201431377 sf1201430377 12 1431377 1.26E-39 NA
vg0704142365 sf0704141366 7 4142365 2.75E-39 NA
Unknow sf0435235465 Unknow Unknow 9.95E-39 NA
vg0719057980 sf0719056987 7 19057980 NA 1.51E-16
vg0719071513 sf0719070520 7 19071513 NA 1.03E-11
vg0718961965 sf0718960972 7 18961965 NA 4.28E-11
vg0719449907 sf0719448914 7 19449907 NA 1.91E-08
vg0719105731 sf0719104738 7 19105731 NA 4.09E-08
vg0719348450 sf0719347457 7 19348450 NA 3.53E-07
vg0719154140 sf0719153147 7 19154140 NA 4.52E-07
vg0420368455 sf0420196499 4 20368455 NA 3.01E-06
vg0520634158 sf0520571599 5 20634158 NA 3.92E-06
vg0414030990 sf0414021705 4 14030990 NA 4.07E-06
vg0216246008 sf0216240138 2 16246008 NA 4.66E-06