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 mr1445 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
vg0105205583 sf0105204583 1 5205583 1.45E-07 1.45E-07
vg0901473638 sf0901472638 9 1473638 5.41E-07 5.41E-07
vg1117584893 sf1117118750 11 17584893 8.36E-07 8.36E-07
vg1117298595 sf1116832447 11 17298595 1.08E-06 1.08E-06
vg0609106093 sf0609105094 6 9106093 2.72E-06 2.72E-06
vg0519670973 sf0519608457 5 19670973 3.12E-06 3.12E-06
vg0131805898 sf0131804854 1 31805898 4.43E-06 4.43E-06