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 mr1958 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
vg1118828056 sf1118361864 11 18828056 2.98E-09 1.13E-06
vg0329183619 sf0329176671 3 29183619 1.51E-08 NA
vg1217949623 sf1217921057 12 17949623 2.88E-08 NA
vg1117444694 sf1116978549 11 17444694 4.11E-08 NA
vg0108399170 sf0108398170 1 8399170 4.34E-08 NA
vg1217748201 sf1217719637 12 17748201 8.29E-07 NA
vg1126585651 sf1126114066 11 26585651 9.46E-06 NA