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 mr1857 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
vg0321163507 sf0321162017 3 21163507 5.58E-10 NA
vg1218085065 sf1218056501 12 18085065 8.77E-09 NA
vg0321780200 sf0321778710 3 21780200 1.21E-08 7.55E-07
vg0816784758 sf0816782044 8 16784758 2.51E-08 NA
vg0715383438 sf0715382445 7 15383438 3.62E-08 NA
vg0721912854 sf0721911861 7 21912854 9.43E-08 NA
vg0913504451 sf0913503450 9 13504451 4.80E-07 1.69E-06
vg0623311841 sf0623310844 6 23311841 8.18E-06 NA
vg0321961541 sf0321960048 3 21961541 NA 5.80E-08