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 mr1236 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
vg0217023273 sf0217017403 2 17023273 1.03E-17 1.34E-11
vg0900337327 sf0900336327 9 337327 1.95E-14 4.59E-08
vg1202070344 sf1202069342 12 2070344 1.00E-13 1.49E-08
vg1114596727 sf1114133045 11 14596727 1.48E-12 8.87E-06
vg1220236581 sf1220208023 12 20236581 1.85E-10 NA
vg1207456835 sf1207454241 12 7456835 5.49E-10 1.93E-06
vg0217349880 sf0217344010 2 17349880 4.70E-09 4.85E-06
vg0106686481 sf0106685481 1 6686481 2.31E-07 3.73E-06
vg0132411125 sf0132410081 1 32411125 3.77E-07 6.62E-06
vg0626990679 sf0626989682 6 26990679 8.77E-06 1.72E-06
vg0106181301 sf0106180301 1 6181301 NA 3.09E-06