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 mr1673 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
vg1206953771 sf1206952661 12 6953771 3.89E-07 3.90E-07
vg0500436518 sf0500436518 5 436518 5.60E-07 5.59E-07
vg1205680656 sf1205679638 12 5680656 1.76E-06 1.75E-06
vg0332527715 sf0332520588 3 32527715 1.91E-06 1.90E-06
vg1126207407 sf1125735821 11 26207407 2.04E-06 2.04E-06
vg0414315785 sf0414306498 4 14315785 3.33E-06 3.34E-06
vg0224663540 sf0224657671 2 24663540 3.40E-06 3.40E-06