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 mr1846 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
vg0411150618 sf0411141319 4 11150618 1.75E-30 8.45E-12
vg0410955533 sf0410946234 4 10955533 3.05E-30 6.81E-12
vg0408524000 sf0408519273 4 8524000 3.94E-26 1.69E-08
vg0407554949 sf0407550218 4 7554949 1.29E-25 9.63E-10
vg0414006438 sf0413997153 4 14006438 1.96E-20 3.11E-06
vg0614462540 sf0614461541 6 14462540 1.60E-19 NA
vg1115982424 sf1115517296 11 15982424 7.19E-16 1.82E-07
vg0131722579 sf0131721535 1 31722579 2.95E-11 2.04E-06
vg0411410586 sf0411401287 4 11410586 NA 4.53E-11
vg0407132799 sf0407128069 4 7132799 NA 1.41E-10
vg1011741385 sf1011670200 10 11741385 NA 4.44E-07
vg1128511488 sf1127988267 11 28511488 NA 2.76E-06
vg0406265203 sf0406260643 4 6265203 NA 4.36E-06
vg0622804797 sf0622803800 6 22804797 NA 4.44E-06