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 mr1525 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
vg0405540593 sf0405536034 4 5540593 1.48E-16 3.32E-14
vg0405445291 sf0405440732 4 5445291 5.97E-11 4.21E-10
vg0405532937 sf0405528378 4 5532937 9.28E-11 2.75E-13
vg0406038377 sf0406033816 4 6038377 1.27E-10 7.76E-07
vg0410128864 sf0410119561 4 10128864 2.20E-10 9.01E-09
vg0405719474 sf0405714913 4 5719474 2.69E-10 3.59E-11
vg0406010273 sf0406005712 4 6010273 3.94E-10 5.89E-07
vg0405386396 sf0405381837 4 5386396 5.63E-10 5.85E-09
vg1004708904 sf1004725441 10 4708904 9.62E-08 1.61E-06
vg0405599476 sf0405594917 4 5599476 1.11E-07 6.35E-16
vg0218297603 sf0218291734 2 18297603 2.76E-07 3.56E-06
vg0404875536 sf0404870975 4 4875536 1.20E-06 1.57E-06
vg0315367742 sf0315366389 3 15367742 2.43E-06 NA
vg0409303280 sf0409298553 4 9303280 NA 1.84E-07
vg0810585964 sf0810584968 8 10585964 NA 4.32E-07
vg0411942900 sf0411933611 4 11942900 NA 6.73E-07
vg0307641865 sf0307640803 3 7641865 NA 1.11E-06
vg0410985561 sf0410976262 4 10985561 NA 1.66E-06
vg0916170022 sf0916169021 9 16170022 NA 1.99E-06
vg1119666919 sf1119200607 11 19666919 NA 3.42E-06
vg0405152405 sf0405147847 4 5152405 NA 4.04E-06
vg1117527349 sf1117061204 11 17527349 NA 9.76E-06