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 mr1792 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
vg1210583868 sf1210581281 12 10583868 3.63E-08 2.91E-07
vg1014025113 sf1013953879 10 14025113 4.03E-08 5.35E-06
vg1210657384 sf1210654797 12 10657384 5.00E-08 3.23E-08
vg1014019486 sf1013948252 10 14019486 5.54E-08 4.23E-06
vg0912631853 sf0912630852 9 12631853 8.98E-08 2.94E-06
vg1215975950 sf1215973246 12 15975950 9.06E-08 9.00E-07
vg1223910416 sf1223876869 12 23910416 9.59E-08 3.25E-06
vg0503455480 sf0503455457 5 3455480 2.80E-07 2.43E-07
vg1217578638 sf1217572593 12 17578638 3.56E-07 4.75E-07
vg0623427584 sf0623426587 6 23427584 4.35E-06 4.80E-07