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 mr1629 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
vg0107766597 sf0107765597 1 7766597 9.09E-10 NA
vg0122872166 sf0122871122 1 22872166 2.11E-09 NA
vg0313792499 sf0313791216 3 13792499 2.66E-09 NA
vg1121822027 sf1121355904 11 21822027 2.74E-09 NA
vg0420735370 sf0420563413 4 20735370 3.10E-09 NA
vg0124173863 sf0124172819 1 24173863 NA 1.03E-06