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 mr1267 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
vg0420711795 sf0420539838 4 20711795 1.56E-08 1.56E-08
vg0421344668 sf0421172722 4 21344668 4.16E-08 4.16E-08
vg0421384856 sf0421212909 4 21384856 2.78E-07 2.78E-07
vg0601322490 sf0601321491 6 1322490 4.00E-07 4.00E-07
vg1006628058 sf1006643681 10 6628058 8.91E-07 8.91E-07
vg0235581681 sf0235575812 2 35581681 1.28E-06 1.28E-06
vg0623981969 sf0623980972 6 23981969 1.31E-06 1.31E-06
vg0210040759 sf0210040757 2 10040759 1.39E-06 1.39E-06
vg0405251670 sf0421275383 4 5251670 1.99E-06 1.99E-06
vg0421021706 sf0420849759 4 21021706 2.61E-06 2.61E-06
vg0517733302 sf0517672943 5 17733302 3.10E-06 3.10E-06
vg0517733387 sf0517673028 5 17733387 4.47E-06 4.47E-06
vg0819985028 sf0819982315 8 19985028 4.60E-06 4.60E-06
vg0400019945 sf0400018945 4 19945 4.95E-06 4.95E-06