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 mr1227 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
vg0315178899 sf0315177546 3 15178899 1.78E-08 2.91E-06
vg0108674689 sf0108673689 1 8674689 1.84E-08 NA
vg0820513390 sf0820510677 8 20513390 3.34E-08 NA
vg1217915087 sf1217886521 12 17915087 3.35E-08 NA
vg0226136784 sf0226130915 2 26136784 6.15E-08 NA
vg1202102394 sf1202101392 12 2102394 2.92E-07 3.18E-06
vg1119398753 sf1118932441 11 19398753 5.85E-07 4.99E-06
vg0624862159 sf0624861162 6 24862159 1.55E-06 1.83E-06