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 mr1601 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
vg0601988659 sf0601987660 6 1988659 1.28E-08 1.28E-08
vg0320459404 sf0320457915 3 20459404 1.11E-07 1.11E-07
vg1212721356 sf1212718695 12 12721356 1.70E-07 1.70E-07
vg0113681497 sf0113680471 1 13681497 8.11E-07 8.11E-07
vg1217569213 sf1217563168 12 17569213 9.41E-07 9.42E-07
vg0820053743 sf0820051030 8 20053743 1.06E-06 1.06E-06
vg0626879239 sf0626878242 6 26879239 1.58E-06 1.58E-06
vg1128987468 sf1128464247 11 28987468 2.00E-06 2.00E-06
vg0824869424 sf0824866710 8 24869424 2.07E-06 2.08E-06
vg0819479739 sf0819477026 8 19479739 2.34E-06 2.34E-06
vg0805513304 sf0805512307 8 5513304 2.50E-06 2.50E-06
vg0826947091 sf0826944377 8 26947091 2.58E-06 2.58E-06
vg0719999922 sf0719998929 7 19999922 2.82E-06 2.82E-06
Unknow sf1128497008 Unknow Unknow 2.84E-06 2.84E-06
vg0903570719 sf0903569719 9 3570719 3.30E-06 3.31E-06
vg0431440861 sf0431255759 4 31440861 3.58E-06 3.58E-06
vg1217863038 sf1217834472 12 17863038 4.11E-06 4.12E-06
vg1208116243 sf1208113649 12 8116243 4.80E-06 4.80E-06