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 mr1473 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
vg0318856031 sf0318854791 3 18856031 1.36E-07 1.36E-07
vg0714475265 sf0714474272 7 14475265 2.53E-07 2.53E-07
vg0626920669 sf0626919672 6 26920669 3.13E-07 3.13E-07
vg0921954182 sf0921953701 9 21954182 3.47E-07 3.47E-07
vg1019533706 sf1019462230 10 19533706 4.47E-07 4.47E-07
vg0415473298 sf0415463981 4 15473298 4.54E-07 4.54E-07
vg0230574938 sf0230569069 2 30574938 5.71E-07 5.71E-07
vg1215339513 sf1215336811 12 15339513 1.61E-06 1.61E-06
vg0226611449 sf0226605580 2 26611449 1.65E-06 1.65E-06
vg1001912776 sf1001911753 10 1912776 2.25E-06 2.25E-06
vg1004690394 sf1004706931 10 4690394 2.36E-06 2.36E-06
vg1213425621 sf1213422959 12 13425621 2.96E-06 2.96E-06
vg0620619372 sf0620618375 6 20619372 3.65E-06 3.65E-06