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 mr1943 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
vg1117597342 sf1117131199 11 17597342 1.68E-08 1.52E-06
vg1117490526 sf1117024381 11 17490526 1.91E-08 1.64E-06
vg1117554396 sf1117088252 11 17554396 3.10E-08 1.49E-06
vg0813601775 sf0813599060 8 13601775 1.16E-07 4.02E-07
vg0320923321 sf0320921831 3 20923321 3.12E-06 NA