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
vg0604294396 sf0604293397 6 4294396 3.62E-20 1.94E-07
vg0604235753 sf0604234754 6 4235753 4.39E-17 1.73E-08
vg0432212638 sf0432027530 4 32212638 2.27E-16 NA
vg0805128532 sf0805127535 8 5128532 2.95E-16 NA
vg0428801373 sf0428616223 4 28801373 3.16E-16 NA
vg0140053429 sf0140052386 1 40053429 3.44E-15 NA
vg0603584467 sf0603583468 6 3584467 6.85E-12 4.18E-06
vg0433037993 sf0432852880 4 33037993 NA 2.11E-06