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 mr1798 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
vg0402030106 sf0402025702 4 2030106 4.82E-19 2.21E-14
vg0402432151 sf0402427746 4 2432151 7.59E-13 8.77E-10
vg0306242443 sf0306241443 3 6242443 2.40E-12 2.63E-07
vg0922275709 sf0922275228 9 22275709 2.98E-12 2.80E-06
vg0521591128 sf0521528569 5 21591128 2.05E-10 NA
vg1205910324 sf1205909305 12 5910324 1.86E-06 NA
vg0402393946 sf0402389541 4 2393946 NA 1.88E-12
vg1010719593 sf1010648414 10 10719593 NA 3.95E-08
vg0821306745 sf0821304032 8 21306745 NA 7.30E-07
vg0819654266 sf0819651553 8 19654266 NA 1.29E-06
vg0516236934 sf0516179416 5 16236934 NA 1.39E-06
vg0232704669 sf0232698800 2 32704669 NA 1.76E-06
vg0419344636 sf0419172674 4 19344636 NA 4.16E-06