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 mr1165 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
vg1217611967 sf1217605922 12 17611967 3.42E-09 NA
vg0808078578 sf0808077582 8 8078578 1.63E-08 NA
vg0721070672 sf0721069679 7 21070672 2.12E-08 2.07E-06
vg0130089725 sf0130088680 1 30089725 2.55E-08 NA
vg0726964336 sf0726963342 7 26964336 7.46E-08 NA
vg0727849372 sf0727848379 7 27849372 2.69E-07 7.27E-07
vg0611444151 sf0611443152 6 11444151 3.00E-06 1.94E-06
vg0516027549 sf0515970057 5 16027549 NA 3.95E-07
vg0900167315 sf0900166315 9 167315 NA 6.54E-07
vg0335609936 sf0335602805 3 35609936 NA 1.48E-06
vg1112963070 sf1112499391 11 12963070 NA 2.69E-06