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 mr1399 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
vg0517742966 sf0517682607 5 17742966 1.09E-08 4.40E-07
vg0601388018 sf0601387019 6 1388018 8.51E-08 NA
vg0200828346 sf0200828346 2 828346 8.97E-08 NA
vg0223637183 sf0223631314 2 23637183 9.74E-08 NA
vg0715979176 sf0715978183 7 15979176 4.09E-07 NA
vg0919892589 sf0919892108 9 19892589 4.82E-07 7.99E-06
vg0121087326 sf0121086281 1 21087326 1.89E-06 8.74E-06