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 mr1452 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
vg0224822504 sf0224816635 2 24822504 1.20E-07 1.21E-07
vg0224592034 sf0224586165 2 24592034 5.59E-07 5.56E-07
vg1117514629 sf1117048484 11 17514629 6.11E-07 6.13E-07
vg0200658088 sf0200658088 2 658088 7.31E-07 7.31E-07
vg0123795673 sf0123794629 1 23795673 9.27E-07 9.28E-07
vg1107376701 sf1107372446 11 7376701 1.11E-06 1.12E-06
vg1226056282 sf1226022676 12 26056282 3.34E-06 3.35E-06
vg0123436071 sf0123435027 1 23436071 3.37E-06 3.38E-06
vg0110522578 sf0110521554 1 10522578 3.98E-06 4.00E-06
vg0401797247 sf0401792842 4 1797247 4.51E-06 4.53E-06
vg0124347123 sf0124346079 1 24347123 4.63E-06 4.64E-06