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 mr1020 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
vg0107647091 sf0107646091 1 7647091 6.15E-14 6.20E-13
vg0805963116 sf0805962119 8 5963116 2.57E-10 8.70E-07
vg0308205433 sf0308204371 3 8205433 4.32E-10 1.52E-06
vg0234396710 sf0234390841 2 34396710 9.33E-10 2.05E-06
vg1215459700 sf1215456998 12 15459700 1.03E-09 3.32E-07
vg0800324069 sf0800323069 8 324069 6.44E-09 2.85E-06
vg0316492889 sf0316491534 3 16492889 6.81E-09 1.62E-06
vg1118023722 sf1117557580 11 18023722 1.43E-08 1.58E-06
vg0316340968 sf0316339615 3 16340968 1.72E-08 4.36E-06
vg0805992743 sf0805991746 8 5992743 3.23E-08 4.77E-06
vg0316222868 sf0316221516 3 16222868 3.56E-06 2.93E-07
vg0816277263 sf0816274549 8 16277263 NA 1.65E-06
vg0805944879 sf0805943882 8 5944879 NA 4.46E-06