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 mr1807 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
vg0507161305 sf0507161247 5 7161305 6.08E-14 9.90E-08
vg0507129275 sf0507129217 5 7129275 7.79E-14 4.07E-09
vg0507081467 sf0507081409 5 7081467 9.03E-13 4.09E-09
vg0624062700 sf0624061703 6 24062700 6.55E-12 3.01E-08
vg0805548986 sf0805547989 8 5548986 4.70E-11 NA
vg0529082128 sf0529019483 5 29082128 1.01E-10 NA
vg0627881901 sf0627880903 6 27881901 1.18E-10 NA
vg0403835689 sf0403831293 4 3835689 2.42E-09 4.39E-08
vg0304670640 sf0304669642 3 4670640 3.86E-08 NA
vg0507057510 sf0507057452 5 7057510 NA 1.90E-06