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 mr1825 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
vg0500824098 sf0500824080 5 824098 5.27E-12 NA
vg1000515396 sf1000514372 10 515396 5.87E-12 8.80E-06
vg1003814398 sf1003813374 10 3814398 6.48E-11 NA
vg1010732405 sf1010661226 10 10732405 2.63E-10 NA
vg0622757624 sf0622756627 6 22757624 4.61E-10 NA
vg1002767170 sf1002766147 10 2767170 1.93E-09 NA
vg1001478317 sf1001477294 10 1478317 1.46E-08 3.12E-06
vg0414280397 sf0414271110 4 14280397 2.22E-08 NA