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 mr1642 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
vg1115929540 sf1115464410 11 15929540 2.54E-12 NA
vg1227407929 sf1227374329 12 27407929 1.43E-11 3.99E-06
vg1004612953 sf1004629491 10 4612953 2.29E-11 NA
vg0122135979 sf0122134934 1 22135979 2.95E-11 2.90E-06
vg1115522117 sf1115058430 11 15522117 3.72E-11 4.61E-06
vg0413358616 sf0413349327 4 13358616 7.92E-11 NA
vg0304531065 sf0304530067 3 4531065 1.51E-10 1.76E-06
vg0908755951 sf0908754950 9 8755951 1.64E-10 2.58E-06
vg0421025376 sf0420853429 4 21025376 1.91E-10 3.81E-06
vg0313208230 sf0313206948 3 13208230 1.43E-09 NA
vg0500274972 sf0500274972 5 274972 4.29E-09 2.83E-06
vg0720403149 sf0720402156 7 20403149 4.24E-08 NA
vg1200189034 sf1200188034 12 189034 1.23E-07 7.89E-06