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 mr1488 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
vg1117584893 sf1117118750 11 17584893 3.27E-08 3.27E-08
vg0328860235 sf0328853288 3 28860235 3.27E-07 3.27E-07
vg0328906064 sf0328899116 3 28906064 6.64E-07 6.64E-07
vg0504650681 sf0504650658 5 4650681 2.07E-06 2.07E-06
vg0209215223 sf0209215221 2 9215223 4.31E-06 4.31E-06
vg0522014819 sf0521952261 5 22014819 4.82E-06 4.82E-06
vg0623833223 sf0623832226 6 23833223 4.92E-06 4.92E-06