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 mr1972 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
vg0402100710 sf0402096304 4 2100710 4.77E-08 4.77E-08
vg1002941211 sf1002940188 10 2941211 1.29E-07 1.29E-07
vg1002941120 sf1002940097 10 2941120 1.83E-07 1.83E-07
vg0406860866 sf0406856311 4 6860866 2.55E-07 2.55E-07
vg0217652051 sf0217646181 2 17652051 3.11E-07 3.11E-07
vg0712648528 sf0712647535 7 12648528 3.17E-07 3.17E-07
vg0406883539 sf0406878798 4 6883539 8.07E-07 8.07E-07
vg0132416907 sf0132415863 1 32416907 1.25E-06 1.25E-06
vg0327981236 sf0327974290 3 27981236 1.38E-06 1.38E-06
vg1117431373 sf1116965228 11 17431373 1.82E-06 1.82E-06
vg1111043318 sf1111037635 11 11043318 1.94E-06 1.94E-06
vg0615329006 sf0615328007 6 15329006 1.96E-06 1.96E-06
vg0910768444 sf0910767443 9 10768444 2.57E-06 2.57E-06
vg0216380020 sf0216374150 2 16380020 4.41E-06 4.41E-06