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 mr1014 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
vg0118347734 sf0118346688 1 18347734 1.32E-07 1.32E-07
vg0203254325 sf0203254323 2 3254325 1.33E-07 1.33E-07
vg0103511143 sf0103510143 1 3511143 7.63E-07 7.63E-07
vg0916695636 sf0916694635 9 16695636 9.88E-07 9.88E-07
vg0921364041 sf0921363560 9 21364041 2.51E-06 2.51E-06
vg0517004979 sf0516944620 5 17004979 4.50E-06 4.50E-06