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 mr1425 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
vg0506633081 sf0506633022 5 6633081 1.85E-08 9.73E-06
vg0901629789 sf0901628789 9 1629789 2.02E-08 4.63E-06
vg0111641654 sf0111640628 1 11641654 9.54E-08 NA
vg0901034419 sf0901033419 9 1034419 3.47E-07 NA
vg0141267197 sf0141266154 1 41267197 8.96E-07 6.55E-08
vg0209659963 sf0209659961 2 9659963 2.20E-06 8.77E-07
vg0723243814 sf0723242821 7 23243814 4.33E-06 5.28E-07
vg0235267445 sf0235261576 2 35267445 5.07E-06 1.81E-06
vg0608948576 sf0608947577 6 8948576 7.86E-06 NA