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 mr1136 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
vg0235365192 sf0235359323 2 35365192 5.84E-15 1.14E-08
vg0319088761 sf0319087521 3 19088761 4.56E-13 2.43E-07
vg0725037095 sf0725036101 7 25037095 1.37E-12 8.02E-07
vg0622020773 sf0622019776 6 22020773 6.20E-12 4.10E-06
vg1108783862 sf1108778472 11 8783862 2.07E-11 4.38E-07
vg1022010131 sf1021938606 10 22010131 3.51E-10 1.23E-06
vg0229221640 sf0229215771 2 29221640 8.36E-07 6.83E-06
vg0219416709 sf0219410841 2 19416709 NA 1.55E-06
vg0804452573 sf0804451576 8 4452573 NA 4.58E-06