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 mr1945 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
vg0815598113 sf0815595399 8 15598113 2.84E-07 2.84E-07
vg0813601775 sf0813599060 8 13601775 2.20E-06 2.20E-06
vg1125606803 sf1125140642 11 25606803 2.83E-06 2.83E-06
vg0815758889 sf0815756175 8 15758889 3.05E-06 3.05E-06
vg1125185431 sf1124719271 11 25185431 4.02E-06 4.02E-06
vg0618469761 sf0618468764 6 18469761 4.68E-06 4.68E-06
vg1215273070 sf1215270368 12 15273070 5.21E-06 5.21E-06