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 mr1576 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
vg0313641931 sf0313640648 3 13641931 3.90E-10 1.57E-07
vg1219410423 sf1219381893 12 19410423 1.32E-09 7.03E-07
vg1017210888 sf1017139661 10 17210888 1.40E-09 4.75E-07
vg0115920715 sf0115919689 1 15920715 3.89E-09 2.98E-06
vg0420286185 sf0420114230 4 20286185 1.01E-08 4.83E-06
vg1219410791 sf1219382261 12 19410791 NA 8.63E-07
vg1206852097 sf1206850987 12 6852097 NA 4.27E-06
vg1218068502 sf1218039938 12 18068502 NA 4.56E-06