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 mr1674 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
vg0420836195 sf0420664238 4 20836195 2.19E-07 2.20E-07
vg1213499508 sf1213496846 12 13499508 3.14E-07 3.15E-07
vg0420823688 sf0420651731 4 20823688 6.47E-07 6.43E-07
vg0330347408 sf0330340447 3 30347408 8.80E-07 8.78E-07
vg0402104951 sf0402100545 4 2104951 1.44E-06 1.44E-06
vg0122790557 sf0122789513 1 22790557 1.49E-06 1.49E-06
vg0910252196 sf0910251195 9 10252196 1.71E-06 1.71E-06
vg0113762419 sf0113761393 1 13762419 3.36E-06 3.35E-06
vg0827935818 sf0827933104 8 27935818 3.95E-06 3.95E-06
vg1215352883 sf1215350181 12 15352883 4.47E-06 4.46E-06