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 mr1485 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
vg0604141030 sf0604140031 6 4141030 9.73E-09 NA
vg0105159820 sf0105158820 1 5159820 3.26E-08 NA
vg0819078104 sf0819075391 8 19078104 4.04E-08 NA
vg0703631746 sf0703630747 7 3631746 2.11E-07 2.52E-06
vg1215653812 sf1215651109 12 15653812 5.00E-06 2.34E-06
vg1218169348 sf1218140784 12 18169348 5.65E-06 1.62E-06
vg1216285021 sf1216282317 12 16285021 NA 2.11E-06
vg0626485579 sf0626484582 6 26485579 NA 5.29E-06
vg0420830218 sf0420658261 4 20830218 NA 8.01E-06