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 mr1611 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
vg0604742724 sf0604741725 6 4742724 9.34E-20 5.59E-08
vg0326933756 sf0326926809 3 26933756 1.42E-17 NA
vg0604236285 sf0604235286 6 4236285 5.89E-17 7.54E-09
vg0311232363 sf0311231081 3 11232363 7.13E-17 NA
vg1118228591 sf1117762449 11 18228591 5.10E-16 NA
vg0805183397 sf0805182400 8 5183397 5.71E-16 NA
vg1123557205 sf1123091075 11 23557205 1.61E-13 NA
vg0314891809 sf0314890456 3 14891809 NA 6.90E-07
vg1006612280 sf1006627903 10 6612280 NA 4.10E-06