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 mr1807 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
vg0519790388 sf0519727872 5 19790388 4.65E-10 NA
vg0216568082 sf0216562212 2 16568082 1.10E-09 NA
vg0128495725 sf0128494680 1 28495725 1.35E-09 NA
vg1227407929 sf1227374329 12 27407929 1.54E-09 NA
vg0211320189 sf0211320186 2 11320189 5.37E-09 NA
vg1019652431 sf1019580933 10 19652431 5.16E-08 NA
vg0128511406 sf0128510361 1 28511406 1.93E-07 NA
vg0417444653 sf0417272695 4 17444653 4.79E-07 NA
vg0622243124 sf0622242127 6 22243124 NA 2.39E-07