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 mr1124 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
vg0506497050 sf0506496991 5 6497050 5.20E-10 1.24E-07
vg0506503838 sf0506503779 5 6503838 5.38E-10 6.45E-08
vg1208638766 sf1208636173 12 8638766 2.11E-09 NA
vg0129623819 sf0129622774 1 29623819 4.36E-09 5.81E-09
vg0604659253 sf0604658254 6 4659253 1.69E-08 NA
vg1215688513 sf1215685810 12 15688513 9.75E-08 NA
vg1115643952 sf1115180261 11 15643952 1.61E-06 2.54E-06
vg1115560507 sf1115096819 11 15560507 1.63E-06 2.59E-06
vg0228320179 sf0228314310 2 28320179 NA 2.18E-08
vg0129591345 sf0129590300 1 29591345 NA 3.12E-07
vg0630442875 sf0630441877 6 30442875 NA 6.94E-07
vg0802334748 sf0802333751 8 2334748 NA 4.75E-06