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 mr1583 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
vg0610549621 sf0610548622 6 10549621 3.75E-36 2.58E-14
vg0610490380 sf0610489381 6 10490380 4.63E-36 3.05E-14
vg0616573493 sf0616572495 6 16573493 4.22E-24 NA
vg0621680835 sf0621679838 6 21680835 7.23E-23 NA
vg0624749710 sf0624748713 6 24749710 4.95E-22 NA
vg0614788218 sf0614787219 6 14788218 9.44E-22 1.05E-06
vg0719601158 sf0719600165 7 19601158 1.03E-21 NA
vg0720195420 sf0720194427 7 20195420 5.18E-18 NA
vg0610803038 sf0610802039 6 10803038 3.23E-16 2.09E-09
vg0610020253 sf0610019254 6 10020253 NA 6.19E-09
vg0610183024 sf0610182025 6 10183024 NA 2.56E-07
vg0613868213 sf0613867214 6 13868213 NA 1.30E-06
vg0121587946 sf0121586901 1 21587946 NA 2.38E-06
vg0610730805 sf0610729806 6 10730805 NA 2.41E-06
vg1217649778 sf1217643733 12 17649778 NA 2.50E-06
vg1217596458 sf1217590413 12 17596458 NA 2.84E-06
vg0610912711 sf0610911712 6 10912711 NA 3.72E-06
vg0205188615 sf0205188612 2 5188615 NA 4.32E-06