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 mr1569 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
vg0710331865 sf0710330871 7 10331865 1.26E-07 1.26E-07
vg0127705431 sf0127704387 1 27705431 4.27E-07 4.27E-07
vg0130451404 sf0130450360 1 30451404 1.61E-06 1.61E-06
vg0207908595 sf0207908594 2 7908595 2.33E-06 2.33E-06
vg0431453051 sf0431267949 4 31453051 2.51E-06 2.51E-06
vg0710610393 sf0710609399 7 10610393 3.76E-06 3.76E-06