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 mr1557 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
vg0918922771 sf0918921771 9 18922771 1.53E-33 1.03E-22
vg1103575882 sf1103571785 11 3575882 4.76E-15 1.85E-06
vg0920514071 sf0920513590 9 20514071 7.30E-14 5.00E-06
vg0917229302 sf0917228301 9 17229302 1.60E-13 7.63E-06
vg0208168116 sf0208168115 2 8168116 4.19E-13 NA
vg0919230563 sf0919230153 9 19230563 1.43E-12 5.12E-08
vg0918998633 sf0918997633 9 18998633 4.17E-12 5.10E-07
vg0326469301 sf0326462395 3 26469301 6.00E-12 NA
vg0808869093 sf0808868097 8 8869093 2.17E-08 NA
vg0918711324 sf0918710324 9 18711324 NA 2.00E-09
vg0224432257 sf0224426388 2 24432257 NA 3.74E-06