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 mr1606 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
vg1213478487 sf1213475825 12 13478487 3.94E-10 2.02E-06
vg1214120133 sf1214117473 12 14120133 3.66E-09 NA
vg1213226344 sf1213223682 12 13226344 4.15E-09 3.40E-06
vg0922414567 sf0922414086 9 22414567 4.32E-09 NA
vg0222160124 sf0222154255 2 22160124 4.38E-09 NA
vg0401607740 sf0401603289 4 1607740 5.08E-09 NA
vg0727264585 sf0727263591 7 27264585 5.73E-08 NA
vg1016658649 sf1016587422 10 16658649 NA 5.92E-07
vg1214404531 sf1214401872 12 14404531 NA 1.13E-06