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 mr1225 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
vg0719048035 sf0719047042 7 19048035 1.03E-15 2.07E-13
vg1214801425 sf1214798766 12 14801425 3.17E-09 2.97E-06
vg1115764925 sf1115301234 11 15764925 2.27E-08 5.62E-06
vg0221955252 sf0221949383 2 21955252 4.42E-08 NA
vg0918940911 sf0918939911 9 18940911 5.23E-08 NA
vg0401817725 sf0401813320 4 1817725 4.35E-07 3.10E-06