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 mr1283 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
vg0700312059 sf0700311059 7 312059 2.70E-09 4.44E-06
vg0315310293 sf0315308940 3 15310293 3.47E-08 NA
vg0426278854 sf0426093727 4 26278854 9.11E-08 NA
vg0316985667 sf0316984541 3 16985667 4.81E-06 4.35E-07
vg0528509176 sf0528446531 5 28509176 6.70E-06 NA
vg0826494037 sf0826491323 8 26494037 NA 3.62E-07
vg1016644917 sf1016573690 10 16644917 NA 7.16E-06
vg1125636908 sf1125170747 11 25636908 NA 7.28E-06