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 mr1655 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
vg0124089174 sf0124088130 1 24089174 1.41E-07 1.41E-07
vg0219777925 sf0219772057 2 19777925 3.86E-07 3.86E-07
vg0819431872 sf0819429159 8 19431872 4.88E-07 4.88E-07
vg0222337580 sf0222331711 2 22337580 7.88E-07 7.88E-07
vg0901536547 sf0901535547 9 1536547 1.45E-06 1.45E-06
vg0220287168 sf0220281300 2 20287168 1.68E-06 1.68E-06
vg0203448916 sf0203448914 2 3448916 2.07E-06 2.07E-06
vg0220941584 sf0220935716 2 20941584 2.81E-06 2.81E-06
vg0819150140 sf0819147427 8 19150140 3.75E-06 3.75E-06
vg0416930919 sf0416758961 4 16930919 3.98E-06 3.98E-06
vg0431016407 sf0430831287 4 31016407 4.54E-06 4.54E-06