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 mr1347 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
vg0429999261 sf0429814128 4 29999261 5.82E-30 2.88E-15
vg0429870242 sf0429685112 4 29870242 2.90E-27 7.64E-16
vg0308626481 sf0308625419 3 8626481 1.36E-12 NA
vg1014775956 sf1014704722 10 14775956 1.96E-12 NA
vg1104306448 sf1104302350 11 4306448 3.89E-12 NA
vg0431147390 sf0430962281 4 31147390 5.98E-12 NA
vg0311462737 sf0311461455 3 11462737 2.04E-09 NA
vg0416558845 sf0416386886 4 16558845 9.80E-08 NA
vg0727254954 sf0727253960 7 27254954 NA 1.47E-06
vg1221736592 sf1221703139 12 21736592 NA 2.73E-06