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 mr1973 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
vg0607415578 sf0607414579 6 7415578 3.79E-136 2.66E-23
vg0428552129 sf0428366981 4 28552129 2.95E-101 NA
vg0717362404 sf0717361411 7 17362404 4.12E-101 3.44E-13
vg0708676935 sf0708675940 7 8676935 3.16E-96 NA
vg0306025759 sf0306024759 3 6025759 8.04E-96 NA
vg0607252722 sf0607251723 6 7252722 NA 1.80E-13
vg0607242219 sf0607241220 6 7242219 NA 3.74E-13
vg0606969001 sf0606968002 6 6969001 NA 6.59E-09
vg0612943263 sf0612942264 6 12943263 NA 2.74E-07
vg1110072677 sf1110067254 11 10072677 NA 1.72E-06
vg1110074178 sf1110068755 11 10074178 NA 1.82E-06
vg0617222044 sf0617221047 6 17222044 NA 1.98E-06
vg0612517051 sf0612516052 6 12517051 NA 2.99E-06
vg0327582306 sf0327575359 3 27582306 NA 3.47E-06
vg1017284750 sf1017213523 10 17284750 NA 3.69E-06
vg0410563090 sf0410553789 4 10563090 NA 4.18E-06
vg0131651142 sf0131650098 1 31651142 NA 5.00E-06