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 mr1419 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
vg0902107236 sf0902106236 9 2107236 5.45E-09 3.19E-06
vg0915815139 sf0915814138 9 15815139 5.75E-09 5.90E-06
vg0801628860 sf0801627862 8 1628860 6.42E-09 NA
vg0102141172 sf0102140172 1 2141172 6.63E-09 NA
vg0528836237 sf0528773592 5 28836237 7.73E-09 NA
vg0223518528 sf0223512659 2 23518528 2.26E-06 3.25E-06
vg0820873126 sf0820870413 8 20873126 7.04E-06 NA