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 mr1468 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
vg0506632837 sf0506632778 5 6632837 8.94E-08 NA
vg0709655042 sf0709654048 7 9655042 1.46E-07 4.82E-07
vg0214178657 sf0214172787 2 14178657 6.76E-07 4.52E-06
vg0140997622 sf0140996579 1 40997622 5.07E-06 8.55E-07
vg0715227873 sf0715226880 7 15227873 NA 3.36E-06