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 mr1299 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
vg0106581088 sf0106580088 1 6581088 8.26E-12 NA
vg0317137871 sf0317136685 3 17137871 4.53E-11 NA
vg0304598567 sf0304597569 3 4598567 1.08E-10 NA
vg0626096352 sf0626095355 6 26096352 1.25E-10 NA
vg0805064661 sf0805063664 8 5064661 1.51E-10 NA
vg0115887532 sf0115886506 1 15887532 1.12E-08 2.42E-06
vg0819439794 sf0819437081 8 19439794 1.26E-08 NA
vg0805950842 sf0805949845 8 5950842 2.91E-08 2.47E-07
vg0528836237 sf0528773592 5 28836237 NA 1.64E-07
vg1215048657 sf1215045999 12 15048657 NA 2.62E-06
vg0227651615 sf0227645746 2 27651615 NA 4.10E-06
vg0906308651 sf0906307651 9 6308651 NA 4.29E-06
vg0205546443 sf0205546443 2 5546443 NA 4.62E-06