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 mr1636 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
vg0205284721 sf0205284719 2 5284721 1.13E-21 1.79E-09
vg0215098426 sf0215092556 2 15098426 2.17E-16 NA
vg0208281695 sf0208281694 2 8281695 6.08E-16 NA
vg0321873075 sf0321871585 3 21873075 7.08E-16 NA
vg0132947824 sf0132946780 1 32947824 1.60E-15 NA
vg0819104489 sf0819101776 8 19104489 5.60E-14 5.90E-06
vg0205293173 sf0205293171 2 5293173 NA 2.18E-06