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 mr1866 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
vg1200594974 sf1200593974 12 594974 9.80E-08 9.80E-08
vg0406886096 sf0406881355 4 6886096 1.70E-07 1.70E-07
vg1118170898 sf1117704756 11 18170898 4.65E-07 4.65E-07
vg1205533524 sf1205532510 12 5533524 4.68E-07 4.68E-07
vg0117092341 sf0117091295 1 17092341 5.15E-07 5.15E-07
vg0324573058 sf0324571137 3 24573058 5.45E-07 5.45E-07
vg0403991999 sf0403987606 4 3991999 5.70E-07 5.70E-07
vg0406862439 sf0406857884 4 6862439 9.30E-07 9.30E-07
vg0215670936 sf0215665066 2 15670936 9.71E-07 9.71E-07
vg0723409844 sf0723408851 7 23409844 1.01E-06 1.01E-06
vg0222019495 sf0222013626 2 22019495 1.09E-06 1.09E-06
vg0216714952 sf0216709082 2 16714952 1.11E-06 1.11E-06
vg1207412253 sf1207409660 12 7412253 1.18E-06 1.18E-06
vg0219878821 sf0219872953 2 19878821 1.22E-06 1.22E-06
vg1121620243 sf1121154120 11 21620243 1.61E-06 1.61E-06
vg1016458801 sf1016387574 10 16458801 1.83E-06 1.83E-06
vg0507301196 sf0507301138 5 7301196 1.88E-06 1.88E-06
vg0406860650 sf0406856095 4 6860650 2.71E-06 2.71E-06
vg0217551079 sf0217545209 2 17551079 3.56E-06 3.56E-06
vg0405465111 sf0405460552 4 5465111 3.67E-06 3.67E-06
vg1117534766 sf1117068621 11 17534766 3.94E-06 3.94E-06