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 mr1883 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
vg0216346431 sf0216340561 2 16346431 1.02E-07 1.02E-07
vg0812659623 sf0812657448 8 12659623 1.86E-07 1.86E-07
vg0800249554 sf0800248554 8 249554 6.27E-07 6.27E-07
vg0811628032 sf0811627037 8 11628032 1.10E-06 1.10E-06
vg0813660047 sf0813657332 8 13660047 1.30E-06 1.31E-06
vg0224908970 sf0224903101 2 24908970 1.41E-06 1.41E-06
vg0226136784 sf0226130915 2 26136784 1.73E-06 1.73E-06
vg1123860680 sf1123394550 11 23860680 2.25E-06 2.25E-06
vg0228423420 sf0228417551 2 28423420 2.47E-06 2.47E-06
vg0217011702 sf0217005832 2 17011702 3.55E-06 3.55E-06
vg0209160076 sf0209160074 2 9160076 3.84E-06 3.84E-06