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 mr1197 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
vg0316595932 sf0316594577 3 16595932 5.61E-08 5.61E-08
vg0303983091 sf0303982087 3 3983091 1.58E-07 1.58E-07
vg1001247771 sf1001246748 10 1247771 3.05E-07 3.05E-07
vg1019119286 sf1019047843 10 19119286 3.93E-07 3.93E-07
vg0805858743 sf0805857746 8 5858743 7.29E-07 7.29E-07
vg0804076961 sf0804075964 8 4076961 7.50E-07 7.50E-07
vg0334741697 sf0334734567 3 34741697 9.70E-07 9.70E-07
vg1106255697 sf1106251449 11 6255697 1.28E-06 1.28E-06
vg0402405188 sf0402400783 4 2405188 1.33E-06 1.33E-06
vg1013280851 sf1013209620 10 13280851 1.49E-06 1.49E-06
vg0431641580 sf0431456473 4 31641580 1.54E-06 1.54E-06
vg0137283220 sf0137282177 1 37283220 1.85E-06 1.86E-06
vg0214124115 sf0214118245 2 14124115 1.89E-06 1.89E-06
vg1106197748 sf1106193500 11 6197748 2.17E-06 2.17E-06