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 mr1906 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
vg0724004854 sf0724003860 7 24004854 5.70E-07 NA
vg1106375766 sf1106371518 11 6375766 8.11E-07 1.45E-06
vg1105377831 sf1105373582 11 5377831 1.48E-06 4.92E-06
vg0710610393 sf0710609399 7 10610393 2.11E-06 1.37E-06
vg0412512389 sf0412503099 4 12512389 2.64E-06 NA
vg1204560575 sf1204559563 12 4560575 2.93E-06 2.92E-06
vg1124078257 sf1123612127 11 24078257 9.68E-06 5.05E-06