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 mr1530 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
vg1125240423 sf1124774263 11 25240423 8.98E-11 6.25E-08
vg1016267177 sf1016195952 10 16267177 4.55E-10 7.59E-06
vg1116832810 sf1116367689 11 16832810 1.38E-09 7.72E-06
vg1015811135 sf1015739905 10 15811135 2.59E-09 6.86E-07
vg0922444221 sf0922443740 9 22444221 8.88E-09 NA
vg1116395716 sf1115930593 11 16395716 1.46E-08 NA
vg0913482728 sf0913481727 9 13482728 2.50E-08 NA
vg0202891012 sf0202891010 2 2891012 4.24E-07 NA
vg1125264457 sf1124798297 11 25264457 NA 2.33E-06