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 mr1046 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
vg1117625330 sf1117159186 11 17625330 7.34E-08 NA
vg0818577556 sf0818574843 8 18577556 9.41E-08 NA
vg1215235888 sf1218062462 12 15235888 NA 6.03E-07
vg1017085147 sf1017013919 10 17085147 NA 6.72E-07
vg1218127441 sf1218098877 12 18127441 NA 2.32E-06
vg0826159950 sf0826157236 8 26159950 NA 6.05E-06