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 mr1648 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
vg0222337580 sf0222331711 2 22337580 1.23E-07 1.23E-07
vg0221872725 sf0221866856 2 21872725 2.29E-07 2.29E-07
vg0626069357 sf0626068360 6 26069357 3.56E-07 3.56E-07
vg0219769506 sf0219763638 2 19769506 4.12E-07 4.12E-07
vg1118496921 sf1118030779 11 18496921 1.35E-06 1.35E-06
vg1010438190 sf1010367011 10 10438190 1.39E-06 1.39E-06
vg0232486002 sf0232480133 2 32486002 1.45E-06 1.45E-06
vg0431034778 sf0430849662 4 31034778 3.10E-06 3.10E-06
vg1010574532 sf1010503353 10 10574532 4.55E-06 4.55E-06
vg1203245777 sf1203244780 12 3245777 4.61E-06 4.61E-06