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 mr1138 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
vg0724505923 sf0724504929 7 24505923 1.31E-14 3.07E-12
vg0511764056 sf0511763986 5 11764056 7.82E-08 NA
vg0311608068 sf0311606786 3 11608068 5.33E-07 4.96E-06
vg0724427664 sf0724426670 7 24427664 NA 1.29E-07
vg0311608269 sf0311606987 3 11608269 NA 5.28E-07