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 mr1616 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
vg0105521069 sf0105520069 1 5521069 7.91E-09 NA
vg0101042259 sf0101041259 1 1042259 3.62E-08 NA
vg0727584718 sf0727583724 7 27584718 9.68E-08 NA
vg1216110511 sf1216107807 12 16110511 2.05E-07 3.89E-07
vg0709128655 sf0709127661 7 9128655 1.18E-06 NA
vg0221240541 sf0221234673 2 21240541 3.07E-06 2.73E-06
vg0232481318 sf0232475449 2 32481318 3.25E-06 3.41E-07
vg0708797466 sf0708796471 7 8797466 4.64E-06 4.37E-06
vg0517733387 sf0517673028 5 17733387 NA 1.43E-06