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 mr1928 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
vg0142200819 sf0142199775 1 42200819 8.66E-10 NA
vg0722668231 sf0722667238 7 22668231 1.62E-08 NA
vg0627169407 sf0627168410 6 27169407 1.78E-08 NA
vg0226047798 sf0226041929 2 26047798 1.93E-08 NA
vg0610105696 sf0610104697 6 10105696 5.59E-08 NA
vg1221123346 sf1221089896 12 21123346 1.03E-07 5.83E-06
vg0801871198 sf0801870201 8 1871198 1.24E-06 5.85E-06
vg0335272611 sf0335265480 3 35272611 1.70E-06 NA
vg1109870708 sf1109865285 11 9870708 2.30E-06 NA
vg0916428615 sf0916427614 9 16428615 NA 2.41E-06