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 mr1138 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
vg0918168241 sf0918167240 9 18168241 7.78E-14 6.80E-09
vg0916234298 sf0916233297 9 16234298 1.81E-13 4.22E-10
vg0916221666 sf0916220665 9 16221666 1.74E-12 3.10E-10
vg0918877233 sf0918876233 9 18877233 3.58E-11 1.14E-08
vg0430038876 sf0429853747 4 30038876 4.85E-10 NA
vg0218089895 sf0218084026 2 18089895 4.97E-10 3.72E-07
vg0315930935 sf0315929582 3 15930935 1.44E-09 NA
vg0918955127 sf0918954127 9 18955127 1.76E-09 5.49E-07
vg0429945960 sf0429760827 4 29945960 1.93E-09 6.86E-06
vg0219801675 sf0219795807 2 19801675 1.40E-06 4.51E-06
vg0216569373 sf0216563503 2 16569373 2.28E-06 1.70E-06
vg0332136548 sf0332129425 3 32136548 2.50E-06 NA
vg0800596392 sf0800595392 8 596392 NA 2.62E-09
vg0800579516 sf0800578516 8 579516 NA 7.52E-09
vg0624426383 sf0624425386 6 24426383 NA 3.17E-07
vg0624437748 sf0624436751 6 24437748 NA 3.62E-07
vg0218342899 sf0218337030 2 18342899 NA 1.26E-06
vg0331267616 sf0331260501 3 31267616 NA 2.09E-06
vg0420234496 sf0420062542 4 20234496 NA 4.63E-06