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 mr1672 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
vg0400454931 sf0400453929 4 454931 1.56E-19 1.05E-22
vg0138250215 sf0138249172 1 38250215 7.43E-17 2.54E-08
vg0137886722 sf0137885679 1 37886722 4.48E-13 5.51E-08
vg0205437290 sf0205437290 2 5437290 1.93E-08 NA
vg0813660047 sf0813657332 8 13660047 2.88E-08 NA
vg1101369743 sf1101368744 11 1369743 5.73E-08 NA
vg0400362758 sf0400361756 4 362758 6.47E-06 4.96E-06
vg0139660797 sf0139659754 1 39660797 8.86E-06 3.07E-06
vg0400439445 sf0400438443 4 439445 NA 1.86E-17
vg0231817029 sf0231811160 2 31817029 NA 2.29E-07
vg0227169881 sf0227164012 2 27169881 NA 1.38E-06
vg0913385027 sf0913384026 9 13385027 NA 2.53E-06
vg0710140235 sf0710139241 7 10140235 NA 3.52E-06
vg0316166709 sf0316165356 3 16166709 NA 3.74E-06