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 mr1893 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
vg0208883775 sf0208883773 2 8883775 9.06E-15 NA
vg0114152375 sf0114151349 1 14152375 1.35E-14 NA
vg0524492576 sf0524429997 5 24492576 1.75E-14 NA
vg0233684404 sf0233678535 2 33684404 2.84E-14 3.05E-06
vg0805195004 sf0805194007 8 5195004 7.29E-14 NA
vg0909793368 sf0909792367 9 9793368 NA 1.08E-07
vg1103187142 sf1103183045 11 3187142 NA 2.07E-06
vg0118775740 sf0118774695 1 18775740 NA 3.27E-06