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 mr1968 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
vg0800073313 sf0800072313 8 73313 1.32E-20 NA
vg0628752358 sf0628751360 6 28752358 3.53E-20 NA
vg0914377364 sf0914376363 9 14377364 6.64E-20 NA
vg0501665488 sf0501665472 5 1665488 8.24E-20 NA
vg0205303002 sf0205303001 2 5303002 9.68E-20 9.53E-06
vg0205301629 sf0205301628 2 5301629 1.31E-19 3.51E-06
vg0628669362 sf0628668364 6 28669362 2.46E-18 NA
vg0917274658 sf0917273657 9 17274658 1.12E-16 NA
vg0212113401 sf0212113397 2 12113401 4.44E-16 NA
vg0200658088 sf0200658088 2 658088 NA 1.66E-06
vg0142473201 sf0142472157 1 42473201 NA 1.77E-06
vg0701128221 sf0701127221 7 1128221 NA 3.51E-06
vg1000739000 sf1000737976 10 739000 NA 7.88E-06