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 mr1167 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
vg0405710877 sf0405706316 4 5710877 1.92E-15 NA
vg0101490991 sf0101489991 1 1490991 3.67E-14 NA
vg0919811177 sf0919810696 9 19811177 2.62E-13 NA
vg1217043044 sf1217036998 12 17043044 1.14E-12 NA
vg0139829401 sf0139828358 1 39829401 1.22E-12 NA
vg1123782809 sf1123316679 11 23782809 1.82E-10 NA
vg1209154479 sf1209151888 12 9154479 NA 3.03E-06
vg0614629248 sf0614628249 6 14629248 NA 6.04E-06