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 mr1204 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
vg0719011406 sf0719010413 7 19011406 1.15E-14 7.91E-13
vg0719091461 sf0719090468 7 19091461 2.70E-14 1.36E-12
vg0717227488 sf0717226495 7 17227488 5.82E-11 3.08E-08
vg0216351953 sf0216346083 2 16351953 1.53E-09 2.37E-06
vg0719003833 sf0719002840 7 19003833 9.53E-09 2.31E-06
vg0613374729 sf0613373730 6 13374729 9.99E-09 8.12E-07
vg1201545939 sf1201544939 12 1545939 5.09E-08 2.11E-06
vg1210300519 sf1210297932 12 10300519 1.29E-07 2.43E-06
vg0717317743 sf0717316750 7 17317743 2.88E-07 3.96E-06
vg0718883395 sf0718882402 7 18883395 1.03E-06 1.61E-06
vg0224293556 sf0224287687 2 24293556 1.18E-06 1.48E-06
vg0719449907 sf0719448914 7 19449907 1.51E-06 8.28E-07
vg1009471877 sf1009400698 10 9471877 NA 2.36E-06
vg1006742777 sf1006758400 10 6742777 NA 3.95E-06