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 mr1832 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
vg1002090281 sf1002089258 10 2090281 3.08E-09 3.47E-06
vg0623248690 sf0623247693 6 23248690 1.73E-08 NA
vg1117156103 sf1116689955 11 17156103 1.74E-08 NA
vg0329175903 sf0329168955 3 29175903 1.81E-08 9.90E-06
vg0919735674 sf0919735193 9 19735674 2.61E-08 NA
vg0329011396 sf0329004448 3 29011396 NA 9.34E-07
vg0125127326 sf0125126282 1 25127326 NA 1.22E-06