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 mr1662 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
vg1125420730 sf1124954569 11 25420730 8.01E-09 4.59E-07
vg1125243705 sf1124777545 11 25243705 8.04E-09 3.65E-07
vg1122449936 sf1121983807 11 22449936 5.60E-08 5.17E-06
vg1125536503 sf1125070342 11 25536503 1.13E-07 1.47E-06
vg1117425028 sf1116958882 11 17425028 4.26E-06 NA