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 mr1771 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
vg1018567052 sf1018495609 10 18567052 1.73E-63 9.23E-17
vg0516106056 sf0516048540 5 16106056 2.12E-51 2.46E-06
vg0129211258 sf0129210213 1 29211258 5.06E-51 NA
vg1015855481 sf1015784251 10 15855481 9.78E-49 NA
vg0132296582 sf0132295538 1 32296582 1.63E-48 NA
vg0516240465 sf0516182947 5 16240465 3.13E-48 2.39E-06
vg1004831241 sf1004847778 10 4831241 NA 1.59E-06
vg1011720271 sf1011649086 10 11720271 NA 3.04E-06
vg1018466898 sf1018395455 10 18466898 NA 3.22E-06
vg1011718495 sf1011647310 10 11718495 NA 3.44E-06
vg0129211280 sf0129210235 1 29211280 NA 4.05E-06