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 mr1795 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
vg0222742146 sf0222736277 2 22742146 8.22E-22 1.91E-14
vg0222730042 sf0222724173 2 22730042 2.24E-19 1.07E-14
vg0224620629 sf0224614760 2 24620629 2.68E-14 2.48E-08
vg0122663217 sf0122662172 1 22663217 1.31E-12 NA
vg0223979286 sf0223973417 2 23979286 1.25E-10 NA
vg0205087718 sf0205087715 2 5087718 2.77E-10 NA
vg0223172226 sf0223166357 2 23172226 2.98E-10 3.98E-06
vg0618618072 sf0618617075 6 18618072 5.18E-09 2.55E-06
vg0224819438 sf0224813569 2 24819438 2.91E-08 1.54E-06
vg0406948268 sf0406943536 4 6948268 5.00E-08 NA
vg0224382266 sf0224376397 2 24382266 6.74E-08 4.25E-06
vg0527357895 sf0527295251 5 27357895 1.50E-06 NA
vg0222593017 sf0222587148 2 22593017 NA 9.82E-08
vg0714325094 sf0714324101 7 14325094 NA 1.69E-06
vg1215976459 sf1215973755 12 15976459 NA 3.91E-06