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 mr1428 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
vg1117178010 sf1116711862 11 17178010 6.16E-10 1.22E-06
vg0124031212 sf0124030168 1 24031212 4.84E-07 NA
vg0324094127 sf0324092206 3 24094127 4.25E-06 NA
vg1214365446 sf1214362786 12 14365446 NA 6.88E-07
vg0431894769 sf0431709664 4 31894769 NA 1.08E-06