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 mr1919 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
vg0142354163 sf0142353119 1 42354163 9.55E-11 1.70E-07
vg0142347941 sf0142346897 1 42347941 1.06E-10 1.41E-07
vg1116585583 sf1116120461 11 16585583 1.01E-08 6.37E-09
vg0101184761 sf0101183761 1 1184761 3.42E-08 NA
vg0809991680 sf0809990684 8 9991680 1.60E-06 7.24E-07