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 mr1828 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
vg0526204912 sf0526142276 5 26204912 1.34E-90 7.61E-15
vg0526224458 sf0526161822 5 26224458 1.03E-89 1.17E-15
vg0322444574 sf0322443063 3 22444574 4.46E-77 NA
vg0217655714 sf0217649844 2 17655714 1.61E-75 1.16E-06
vg0805873180 sf0805872183 8 5873180 1.46E-74 NA
vg0523464873 sf0523402294 5 23464873 7.77E-73 NA
vg0525016334 sf0524953749 5 25016334 NA 2.77E-08
vg0807387849 sf0807386854 8 7387849 NA 2.83E-06
vg1213796670 sf1213794008 12 13796670 NA 3.54E-06
vg0525113117 sf0525050532 5 25113117 NA 4.30E-06
vg0318147668 sf0318146450 3 18147668 NA 5.91E-06