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 mr1815 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
vg0122207649 sf0122206604 1 22207649 2.12E-11 6.09E-06
vg0139384190 sf0139383147 1 39384190 1.70E-10 5.53E-06
vg1017238242 sf1017167015 10 17238242 5.51E-10 NA
vg0800003353 sf0800002353 8 3353 1.30E-09 NA
vg0414761828 sf0414752542 4 14761828 2.08E-09 NA
vg1207220741 sf1207218137 12 7220741 4.40E-09 4.57E-07
vg1218022752 sf1217994188 12 18022752 NA 1.28E-06
vg0217924215 sf0217918346 2 17924215 NA 3.29E-06
vg0500274972 sf0500274972 5 274972 NA 5.92E-06