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 mr1968 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
vg0808040055 sf0808039059 8 8040055 1.87E-09 7.72E-07
vg1000493003 sf1000491979 10 493003 1.81E-08 NA
vg0723644677 sf0723643684 7 23644677 2.26E-08 2.42E-07
vg0808034898 sf0808033902 8 8034898 8.73E-08 4.81E-06
vg0308391272 sf0308390210 3 8391272 9.50E-08 3.07E-06
vg0527405457 sf0527342813 5 27405457 1.69E-07 5.13E-07
vg0402981114 sf0402976720 4 2981114 1.55E-06 1.00E-06
vg1000539208 sf1000538184 10 539208 7.75E-06 NA
vg0507108805 sf0507108747 5 7108805 NA 1.63E-06
vg0821981777 sf0821979064 8 21981777 NA 2.99E-06