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 mr1397 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
vg0805946030 sf0805945033 8 5946030 7.29E-10 4.59E-08
vg0805005643 sf0805004646 8 5005643 1.13E-09 3.12E-08
vg0804905723 sf0804904726 8 4905723 4.23E-09 8.91E-08
vg0321576069 sf0321574579 3 21576069 7.89E-09 3.47E-08
vg0430691715 sf0430506590 4 30691715 2.67E-08 1.35E-06
vg0124420479 sf0124419435 1 24420479 2.85E-08 7.37E-07
vg0206578247 sf0206578247 2 6578247 5.64E-08 7.66E-07
vg0604014602 sf0604013603 6 4014602 9.49E-08 2.55E-06
vg0329703696 sf0329696736 3 29703696 1.13E-07 1.73E-06
vg1020508138 sf1020436617 10 20508138 1.80E-07 4.89E-06
vg0107079035 sf0107078035 1 7079035 3.21E-07 2.11E-06