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 mr1184 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
vg0332498725 sf0332491598 3 32498725 2.90E-09 NA
vg0815000570 sf0814997856 8 15000570 7.74E-09 NA
vg0922565216 sf0922564735 9 22565216 1.26E-08 NA
vg0603711280 sf0603710281 6 3711280 2.43E-08 NA
vg0107304050 sf0107303050 1 7304050 3.10E-08 NA
vg1126694376 sf1126222763 11 26694376 2.26E-07 6.82E-07
vg0827742572 sf0827739858 8 27742572 NA 1.67E-06
vg0219809349 sf0219803481 2 19809349 NA 1.75E-06
vg0922881564 sf0922881083 9 22881564 NA 2.51E-06