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 mr1631 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
vg0405603570 sf0405599011 4 5603570 2.96E-18 3.32E-12
vg0405571324 sf0405566765 4 5571324 2.65E-16 8.97E-13
vg0405739020 sf0405734459 4 5739020 3.14E-12 7.71E-08
vg0410688931 sf0410679633 4 10688931 1.36E-10 4.31E-07
vg0805209310 sf0805208313 8 5209310 2.25E-10 2.36E-06
vg0409228132 sf0409223405 4 9228132 5.25E-10 4.23E-07
vg0405169454 sf0405164896 4 5169454 2.19E-09 5.59E-07
vg0815817158 sf0815814444 8 15817158 9.94E-09 NA
vg0805159916 sf0805158919 8 5159916 1.82E-07 7.63E-07
vg0621576738 sf0621575741 6 21576738 NA 4.42E-06