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 mr1420 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
vg1117584893 sf1117118750 11 17584893 2.15E-09 2.15E-09
vg0125127326 sf0125126282 1 25127326 7.58E-07 7.59E-07
vg0504650681 sf0504650658 5 4650681 9.91E-07 9.91E-07
vg0522014819 sf0521952261 5 22014819 9.98E-07 9.99E-07
vg0800161026 sf0800160026 8 161026 1.31E-06 1.31E-06
vg0701484527 sf0701483527 7 1484527 1.55E-06 1.55E-06
vg0501367936 sf0501367920 5 1367936 2.25E-06 2.25E-06
vg0714405504 sf0714404511 7 14405504 3.51E-06 3.51E-06
vg0114134418 sf0114133392 1 14134418 3.72E-06 3.72E-06
vg0208293749 sf0208293748 2 8293749 4.53E-06 4.53E-06