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 mr1581 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
vg0816101264 sf0816098550 8 16101264 4.29E-07 4.29E-07
vg0605865870 sf0605864871 6 5865870 1.01E-06 1.01E-06
vg0605892046 sf0605891047 6 5892046 1.56E-06 1.56E-06
vg0517580953 sf0517520596 5 17580953 1.58E-06 1.58E-06
vg1000738531 sf1000737507 10 738531 2.63E-06 2.63E-06
vg0132361776 sf0132360732 1 32361776 4.58E-06 4.58E-06
vg1208226149 sf1208223554 12 8226149 4.63E-06 4.63E-06
vg1208226725 sf1208224130 12 8226725 5.19E-06 5.19E-06